Identifying and Quantifying Ecological Flows with Geomorphic Functions

Ashraf Zaghal1


1 School of Engineering, University of Guelph, 50 Stone Road East
Guelph, Ontario, N1G 2W1, Canada; E-mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it



Recently, proposing environmental flow rules in order to maintain or restore the physical habitats of streams has become commonplace. Structuring ecological objectives and rationale to support such rules remains a challenging task, especially in regard to articulating relationships between hydro-geomorphic processes and ecological functions. Ecological principles and tools that support existing environmental flow methodologies include habitat rating and simulation models, ecological databases, and expert opinion, but often neglected conceptual models that study the interactions amongst hydro-geomorphic processes and ecological functions. Despite well-established tools and concepts that link fluvial geomorphology to stream ecology, restoration practitioners and water managers lack effective and practical guidelines to determine environmental flows with geomorphic functions and restore important ecological functions spatially and temporally. Therefore, this paper presents a conceptual framework that proposes process-based and science-based guidelines to integrate ecological requirements of aquatic organisms into environmental flows with geomorphic functions in gravel-based streams. It is presumed that the framework which is driven by a bimodal conceptual model and a feedback element has potential to improve the ecological basis of environmental flow rules with geomorphic focus and prioritize stream habitat assessment protocols for conservation purposes.

Keywords: habitat, ecological guilds, hydro-geomorphic processes, ecological flow, geomorphic functions.


Degradation of ecological functions in gravel-bed streams has been linked to altered sediment and flow regimes. Aggradation of channel units and the accumulation of sediment in their substrate have negative effects on many ecological requirements of aquatic species in gravel-bed streams. Key ecological requirements include reproduction (Coulombe-Pontbriand and Lapointe, 2004; Wheaton et al., 2004; Escobar-Arias and Pasternak, 2010), feeding (Austen et al., 1994; Gore et al., 2001; Suttle et al., 2004), and living space (Frissel et al., 1986; Wood and Armitage, 1997; Welcomme et al., 2006; Lapointe, 2012). Numerous methodologies have been suggested to determine environmental flows required to protect aquatic ecosystems in streams and rivers (Tennant, 1976; Bovee, 1982; Stalnaker et al., 1995; Richter et al., 1997; King and Louw, 1998; King et al., 2003; Poff et al., 2009). Tharme (2003) categorized environmental flow methodologies into four types: hydrological, habitat rating, habitat simulation, and holistic methodologies. Ecological principles and tools used in the articulation of ecological objectives within these methodologies vary according to assumed linkages between ecology and stream physical processes. Generally speaking, hydrological methodologies and habitat rating methodologies use simple ecological inputs and assumptions, and focus on hydrologic parameters and water depth and velocity as key streamflow variables that affect habitat (Tennant, 1976; Jowett, 1997; Richter et al., 1997; Stewardson and Gippel, 2003). On the other hand, habitat simulation methodologies and holistic methodologies use complex ecological input schemes that may include habitat suitability tools, hydraulic modeling techniques, and field data (Milhous et al., 1989; Hardy, 1998; Harby et al., 2007; Parasiewicz, 2008), ecological hypotheses and databases (Stewardson and Gipple, 2003; Poff et al., 2009), and expert opinion (King and Louw, 1998; King et al., 2003).

Historically, environmental flow rules with focus on hydro-geomorphic processes have proposed channel maintenance flows (Leaf, 1998; Schmidt and Potyondy, 2004) and flushing flows (Reiser et al., 1989; Kondolf and Wilcock, 1996; Ortlep et al., 2003) using sediment entrainment thresholds and bankfull flow characteristics (Wolman and Leopold, 1957; Leopold et al., 1964; Rosgen et al., 1986). Grey- and peer-reviewed literature concerned with hydro-geomorphic processes and environmental flows have generally used qualitative ecological objectives such as "maintaining habitat features" and "restoring ecological integrity" on the basis that moving most of the sediment or maintaining the shape of the channel would maintain overall ecological health and integrity. Kondolf and Wilcock (1996) indicated that one of the key issues that inhibit the success of prescribing effective flushing flows (i.e. streamflows that erode excess fines from channel units and substrate) for ecological purposes is ambiguous ecological objectives. Despite recent literature concerned with identifying environmental flow rules with focus on hydro-geomorphic processes (Stewardson and Gipple, 2003; Escobar-Arias and Pasternak, 2010; Escobar-Arias and Pasternak, 2011), a process-based conceptual approach that integrates ecological requirements of functional groups of aquatic species and their habitat template rather than target species is lacking.

The integration of ecological principles based on ecological databases and/or expert opinion can be a challenging task. Arthington et al. (2006) noted that beside the general lack of site-specific ecological databases, obtaining a precise expert input from ecologists on specific ecological flow requirements could be unattainable because of ecologists' inability to articulate objectives or their reluctance to provide them. The absence of precise and articulate ecological objectives of environmental flow rules may lead to untenable management decisions (Poff et al. 2003; Arthington and Pusey, 2003) and unsuccessful stream restoration initiatives (Wheaton et al., 2004; Kondolf, 2006; Kondolf et al., 2007; Souchon et al., 2008). While habitat simulation models (e.g. PHABSIM and MesoHABSIM) are generally proposed as an ecologically-based tool that can be used within a broader flow management framework (IFIM; Bovee, 1982; Bovee et al., 1998), limitations of these models include their focus on "target" species rather than the entire ecosystem (Arthington and Zalucki, 1998; Souchon and Capra, 2004), focus on the low range of streamflows (Arthington and Zalucki, 1998; Lamouroux et al., 2006), and general lack of examining hydro-geomorphic processes and their influence on fish habitat (Hudson et al., 2003).

In this paper, the review of ecological underpinnings of existing environmental flow methodologies is not meant to discredit or substitute any of them, but to provide rationale for proposing means to structure and integrate ecological requirements into environmental flow rules with geomorphic functions. Tools and models that link ecological principles to fluvial geomorphology exist in the peer-reviewed literature (Frissel et al., 1986; Imhof et al., 1996; Maddock, 1999; Thomson et al., 2001; Newson, 2002; Poole, 2002; Dollar et al., 2007). However, one of the main barriers to using these tools and models as a guidance to integrating ecological requirements into environmental flow rules is their overwhelming complexity and the numerous variables, processes and scales examined, which renders them impractical to use or articulate. Stream restoration practitioners and water managers demand simple, yet scientifically-based tools that provide effective guidelines (Wheaton et al., 2004; Arthington et al., 2006; Wilcock, 2012), and embrace landscape ecology and habitat heterogeneity (Montgomery, 1999; Pool, 2002; Dollar et al., 2007; Buffington, 2012; Lapointe, 2012). Therefore, this paper aims at proposing a process-based conceptual framework that integrates ecological requirements into hydro-geomorphic processes in gravel-bed streams, and identifies ecologically-based flows accordingly.


Materials and Methods

The conceptual framework proposed in this paper has two components: a conceptual model and a feedback element (Figure 1). The conceptual model has two objectives; each objective is defined by a conceptualization mode. The first objective is to integrate processes where fluvial geomorphology, stream ecology and stream hydrology interact to create and maintain habitat structure based on the assumption that streamflow regime is the key driver of hydro-geomorphic processes and habitat structure in gravel-bed streams (Top-Down: causal linkages mode). The second objective is to define an ecological input integration tool that synthesizes and integrates ecological requirements into hydro-geomorphic processes and streamflow regime (Bottom-Up: ecological input mode) (Figure 1). The design of the conceptual model based on top-down and bottom-up approaches help combine two modes of analysis into one model. More specifically, the causal linkages mode helps to develop an understanding of the system as a whole and formulate a process-based overview starting from stream hydrology as the key process or driver and ending with habitat structure as a final product or template. The ecological input mode intends to start with the end result (i.e. habitat structure), synthesize and piece together necessary knowledge concerning habitat structure and develop an understanding of how habitat structure is maintained by hydro-geomorphic processes and streamflow regime.

The feedback element examines and tests the applications of the conceptual model. It consists of quantification of potential ecological flows identified in the conceptual model, validation of ecological flows, and recommending management scenarios accordingly.


Figure 1: The Conceptual Framework including the bimodal conceptual model and the feedback element.


Causal Linkages Mode

Figure 2 proposes three spatial scales of a typical gravel-bed stream with pool-riffle morphology in which contrasts are made between "functional" and "non-functional" habitat units resulting from hydro-geomorphic processes acting on these units. The premise of Figure 2 is that without a "functional" streamflow regime which drives hydro-geomorphic processes at different habitat scales, habitat units would be rendered non-functional. The causal linkages mode in the conceptual model considers streamflow regime as the key driver of the structure and function of stream ecosystems (Bunn and Arthington, 2002; Petts, 2009; Poff et al., 2009; Escobar Arias and Pasternack, 2010). This consideration is based on numerous ecological studies that have shown significant relationships between flow alteration and degradation of ecological functions in stream systems (Poff and Allan, 1995; Poff et al., 1997; Gordon et al., 2004; Petts, 2009; Poff et al., 2009).

The concept of functional habitat has been proposed in the stream ecology literature to address habitat as a surrogate for biota, where a functional habitat is a habitat unit within landscape filters (Poff, 1997). This functional habitat is controlled by a myriad of physical variables (Austen et al., 1994; Harper and Everard, 1998; Montgomery, 1999; Wilcomme et al., 2006; Fisher et al., 2007; Storey and Lynas, 2007). Buffington (2012) proposed four scales of channel change in gravel-bed streams. These scales are: reach, bed form, cross-sectional, and grain-scale adjustment. For the purpose of the conceptual model (including the causal linkages mode and the ecological input mode), two of these scales are proposed, namely, bed form (i.e. pool-riffle mesohabitat) and grain-scale adjustment (i.e. sediment patches) (Figure 2). These two scales of channel change are highlighted because of their critical importance to stream ecology. Buffington (2012) notes that these two scales occur in temporal and spatial scales that are more relevant to aquatic organisms that reach and cross-sectional scales (i.e. shorter and smaller). In a similar vein, research has shown that numerous ecological requirements of aquatic organisms coincide with scales of channel change that are within the mesohabitat scale (Frissel et al., 1986; Poole, 2002; Dollar et al., 2007; Buffington, 2012; Lapointe, 2012). Accordingly, associations between ecological requirements of aquatic organisms, hydrogeomorphic processes (i.e. scales of channel change), and streamflow variability can provide critical information about streamflow requirements for maintaining a functional habitat.

As Figure 2 implies, at the macrohabitat scale, pools may be filled with sediment and pool-riffle diversity (e.g. pool:riffle ratio and number of pools) may be compromised by the lack of hydro-geomorphic processes that are capable of eroding excess sediment and maintaining pool-riffle sequences within a stream segment (Wohl et al., 1993; Sear, 1996; Milan et al., 2001; Rathburn and Wohl, 2003; Wilkenson et al., 2004). Pool-riffle diversity has been proven to be important for multiple habitat needs within the river landscape (i.e. complementation) (Frissel et al., 1986; Imhof et al., 1996; Lapointe, 2012). At the mesohabitat scale, excess sediment in pools may decrease the living space of aquatic organisms demanding shelter and refugia (Imhof et al., 1996; Armstrong et al., 2003) and movement between riffles and pools (Lapointe, 2012). At the microhabitat scale, infilling of substrates may impede reproduction success (Kondolf, 2000; Escobar Arias and Pasternack, 2010), and feeding opportunities (Suttle et al., 2004). Scales beyond the habitat scales shown in Figure 2, such as valley or watershed scales and processes associated with them such as sediment budget, land uses, and geology are beyond the scope of the conceptual model. However, some of these processes such as sediment budget could be integrated into the feedback element for decision making and management purposes.


Figure 2: A schematic showing different habitat scales (i.e. macrohabitat, mesohabitat, and microhabitat) with contrasts between functional and non-functional habitats and scales of channel change (between brackets).


Ecological Input Mode

The ecological input mode is a bottom up approach to define ecological requirements from the perspective of stream ecology. Figure 3 shows the steps needed to run this process, which has the overarching purpose of integrating ecological requirements into stream hydrology and hydro-geomorphic processes, where features and variables are defined in a process-based manner.

According to Figure 3, defining the functional habitat requires the definition of the dominant ecological guilds within the habitat (Step 1) and the geomorphic variables that control this guild (Step 2). The spatial scale of the ecological input mode covers mesohabitats and microhabitats. These scales are most relevant to community regulation and habitat defining processes (Stewardson and Gippel, 2003; Thorp et al., 2006). The functional habitat accordingly is a geomorphic unit (i.e. channel unit, sediment patch) that provides suitable morphology or/and bed material for an ecological need. More specifically, Steps 1 and 2 discuss four functional habitats, their dominant ecological guilds, and geomorphic controls. Figure 4 shows these habitat units, namely pool mesohabitat, riffle mesohabitat, pool microhabitat, and riffle microhabitat.


Figure 3: The bi-modal conceptual model with implementation steps.


The process of dividing streams into habitat units and types is well established in stream ecology and fishery management (Poff, 1997; Rabeni et al., 2002; Noble et al., 2007) on the assumption that the distribution of habitat types at different scales influences the abundance and distribution of aquatic species (Southwood, 1977; Poff, 1997; Welcomme et al., 2006). Accordingly, habitat is used as a surrogate for the biota, which enables the study of ecological requirements of aquatic species based on their functional relationships within the stream system (Poff, 1997). The Functional Habitat Concept (Harper and Everard, 1998; Buffagni et al., 2000) proposes that "conserving habitats ultimately conserves biodiversity". The ecological guild concept groups aquatic organisms according to their habitat needs and the physical variables that affect these needs in river ecosystems (Austen et al., 1994; Welcomme et al., 2006; Noble et al., 2007).


Step 1: Define Ecological Guilds

Step 1 of the ecological input mode defines ecological requirements at different spatial and temporal scales based on the Functional Habitat Concept (FHC) and the ecological guild concept. Using Figure 4, dominant ecological guilds (and typical species) that are mostly influenced by channel morphology and bed material characteristics can be linked to geomorphic units. The ecological guilds investigated in Step 1 are reproductive, feeding, and habitat use guilds (Austen et al., 1994; Noble et al., 2007). Habitat use guilds may represent the aquatic species that utilize the stream for a living, rearing or refuge space such as the need of limnophilic species (e.g. Small cyprinids, smallmouth bass, bluntnose minnow) for deep slow moving water (e.g. pools) (Cunjak and Power, 1986; Imhof et al., 1996; Armstron et al., 2003; Sotiropoulos et al., 2006) and rheophilic species (e.g. Brown trout, Torrent sucker, blacknose dace) which prefer shallow fast flowing water for their habitat use such as riffles (Vadas et al., 2000; Welcomme et al., 2006). Reproduction use guilds include lithophilic species (e.g. salmonids) that have specific substrate size and distribution characteristics (Welcomme et al., 2006), and phytophilic species that use plants in deep water for spawning. Feeding guilds include piscivorous (fish eater), benthivorous (benthic eater), and omnivorous species (all eater) (Noble et al., 2007).


Figure 4: A schematic showing the four main habitat units examined, ecological guilds, and geomorphic controls.


Step 2: Identify Geomorphic unit/Geomorphic control

Step 2 defines geomorphic controls on ecological guilds illustrated in Figure 4. Pool depth is a major ecological requirement for summer and overwintering habitat where cold water species such as trout and warm water species such as smallmouth bass tend to look for cover or thermal refugia (May and Lee, 2004). Pool residual depth, which is the difference in elevation between a pool and the downstream riffle crest, determines the variation in streambed topography between pools and riffles and the stability of riffles in the pool-riffle sequence (Madej, 1999; Cover et al., 2008). Excess sediment in pools decreases pool depth and adjusts channel morphology in a way that habitat use by aquatic organisms is negatively affected by the decrease in available refugia space (Armstrong et al., 2003; May and Lee, 2004); habitat heterogeneity space (Lapointe, 2012), and fish movement (Lonzarich et al., 2000).

Microhabitats are investigated at the sediment patch scale. Sediment patches are small scale habitat units within pools and riffles that have homogenous particle size, water depth, and velocity (Frissel et al., 1986; Boyero, 2003; Pedersen and Friberg, 2007). Associations of this scale with ecological guilds are determined by feeding habits (Gore et al., 2001; Miyake and Nakano, 2002) and reproduction habits (Zimmer and Power, 2006; Welcomme et al., 2006). The guilds at this scale are influenced by changes in substratum type and characteristics. Sediment patch characteristics are critical to many ecological guilds in gravel-bed streams. Reproductive needs including those associated with spawning, incubation and emergence are mostly affected by microhabitat geomorphic controls such as bed material characteristics (e.g. median particle size and sand content (Kondolf, 2000; Suttle et al., 2004; Escobar Arias and Pasternack, 2010). The success of incubation of Salmonids' eggs (i.e. lithophilic species) depends on the percentage of sand in the substrate (Waters, 1995; Kondolf, 2000; Gordon et al., 2004). Feeding guilds at the microhabitat scale are related to feeding habits, which have been shown to correlate with bed material size (Jowett et al., 2003). Juvenile trout (i.e. benthivorous species) prefer substrate with minimal sand content in order to feed on benthic invertebrates residing underneath cobble substrates (Suttle et al., 2004). Allan and Castillo (2007) noted that benthic invertebrates that were cited as a preferred food for salmonids due to their availability on the streambed surface occupy erosional sediment patches with high near bed current (i.e. riffles). Generally speaking, benthic species are sensitive to sedimentation and oxygen depletion because they feed and reproduce in the substrate (Aarts and Nienhuis, 2003). Berkman and Rabeni (1987) found that benthivorous species such as juvenile trout in the feeding guild and lithophilous species such as adult trout in the reproductive guild were more affected by streambed patch sedimentation than other guilds. In a similar study, Sutherland et al. (2002) found that gravel spawners (i.e. lithophilous) are most sensitive to excessive sediment. Cover et al. (2008) found that sand sized particles (i.e. 0.06 mm ≤ particle size ≤ 2 mm) have a negative impact on benthic invertebrates' substrate habitat and fine gravel (i.e. 2 mm ≤ particle size ≤ 4 mm) has also been cited as responsible for embedding cobbles in gravel-bed streams and endangering ecological guilds such as feeding and habitat use for fish and benthic invertebrates, respectively (Imhof et al., 1996; Armstrong et al., 2003; Jowett et al, 2003; Kaller and Hartman, 2004; Suttle et al., 2004).

While the conceptual model has the potential to include different stream and river sizes because of its process-based foundations, Step 2 focuses on small streams and medium rivers with pool-riffle morphology. Key assumption about processes at the macrohabitat scale is that habitat metrics are more pronounced at the mesohabitat and microhabitat scales, accordingly ecological guilds and controls can be aggregated at the reach scale. It should be noted that Figure 4 is not entirely comprehensive. The rationale behind choosing pools and riffles as important functional mesohabitats is that pool-riffle sequences are the characteristic reach scale bedforms of gravel- and mixed-bedded channels of low to moderate slope (Clifford, 1993; Knighton, 1998; Church, 2002).


Step 3: Define Hydro-geomorphic Processes

The objective of Step 3 is to articulate hydro-geomorphic processes necessary to create and restore geomorphic controls. The notion of hydro-geomorphic processes described here refers to those habitat-defining processes of streamflows, which encompass low, medium and high flows, and which have fluvial impact on a functional habitat such as changing channel morphology, mobilizing bed material, and re-sorting sediment patches. Table 1 proposes four scales of change in functional habitat because of hydro-geomorphic processes acting upon them. These scales are erosion in pools, deposition on riffles, grain scale changing in size, packing and protrusion in riffle sediment patches, and grain scale changing in textural patterns in pools. Some of these scales have been illustrated in the context of functional habitat in Figure 2.

Knowledge of hydro-geomorphic processes that maintain and restore functional habitat is fundamental. According to Buffington (2012), scales of channel change include grain scale adjustment, changes in bed topography and bed forms, cross sectional changes, and reach scale changes (e.g. altered stream gradient). Step 3 addresses two of these changes, namely changes in bed forms (i.e. mesohabitat scale: pool-riffle sequences) and grain scale adjustment (i.e. microhabitat scale: sediment patch). Studies investigating the processes responsible for maintaining pool-riffle sequences have proposed many hypotheses (Sear, 1996). The most debated of these hypotheses are the velocity reversal hypothesis and its variations (Keller, 1971; Keller, 1978; Wilkinson et al., 2004; Caamano et al., 2009) and the secondary flow structures hypothesis (Thompson and Wohl, 2009; Nikora, 2010). The velocity reversal hypothesis indicates that at low flows, the velocity over the downstream face of the riffle is higher than through the pool, but as discharge increases, velocity increases at a faster rate through the pool, causing it to exceed the velocity over the riffle (Keller, 1971; Sear, 1996). Reversal in velocity causes reversal in shear stress and sediment entrainment. Accordingly, hydro-geomorphic processes in pool-riffle sequences consist of the movement of sediments from riffles into pools during low flows, and the movement of sediments from pools into riffles during high flows (Wohl et al., 1993; Wilkinson et al., 2004; Thompson and Wohl, 2009; Brown and Pasternack, 2009). Since the velocity reversal hypothesis has been rigorously tested in the literature (Caamano et al., 2009) and since consensus is not often expected in fluvial geomorphology (Wilcock, 2012), the hypothesis is used in the conceptual model as the chief mechanism responsible for the bed form scale change (pool-riffle mesohabitat scale).

At the microhabitat scale, Step 3 focuses on hydro-geomorphic processes that affect grain scale adjustments (Powell, 1998; Miyake and Nakano, 2002; Buffington, 2012), namely local changes in grain size, packing and protrusion (Buffington et al., 1992; Buffington, 2012), and formation of textural patches (Powell, 1998; Buffington and Montgomery, 1999). At this scale of channel change (Table 1), processes may include secondary flow structures (Thompson and Wohl, 2009), and turbulent bursts (Sear, 1996). Buffington (2012) argues that progression of successive scales of channel changes start with grain size adjustment (i.e. bed loosening and changes in grain size) and end in changes in stream gradient with temporal scales extending from seasonal to centennial.




Step 4: Identify Streamflow Regime

Table 2 shows two characteristics of streamflow regime that define the frequency of streamflows driving hydro-geomorphic processes, and the range of streamflows necessary to carry out the process. Table 2 also shows how ecological flows were identified based on the identification of each of the three preceding steps. Previous work on testing the hypotheses of the conceptual model on the Credit River, Ontario, Canada (Zaghal, 2010) demonstrated that the ecological flows identified in Table 2 can be placed within the ranges shown in Figure 5. The flow variability depicted in Figure 5 agrees with typical snowmelt hydrograph observed in unregulated streams and rivers in Ontario and other geographic regions in Canada (De Boer et al., 2005). As presented in Figure 5, pool and riffle flows have a seasonal pattern and they range between medium flows and bankfull flows (bankfull flow is 17 m3/s). Sediment patch flows occur more frequently and they are in the range of low to medium flows, and riparian and floodplain flows are bankfull flow and above.

It has been already noted that the timing of ecological guilds is identified early in the process (e.g. habitat use in winter for limnophilic species). Accordingly, the natural timing of the streamflow regime is set to coincide with ecological needs (i.e. guilds) indicated, similar to the argument of hydrological methodologies with ecological metrics such as (Richter et al., 1997; Poff et al., 1997; Poff et al., 2009) can be inferred from Figure 5, mobilizing fine sediment from pools in the spring may provide summer habitat use for species such as brown trout and brook trout, and mobilizing fine sediment from riffles during summer low flows may provide suitable substrate, with minimum sand content, for benthic invertebrates habitat use.


Figure 5: A typical snowmelt streamflow hydrograph (Credit River, Ontario, Canada) with suggested ecological flows that target different geomorphic units and ecological guilds.




Figure 6: A flow chart representing the process-based Conceptual Framework and the breakdown of its components.


The Feedback Element

Figure 6 shows the overall structure of the conceptual framework; consisting of the conceptual model and the feedback element. Three main phases of the feedback element are proposed. Phase 1 is the quantification of ecological flows (identified in the conceptual model), Phase 2 is the validation of ecological flows, and Phase 3 is identifying management scenarios.


Phase 1: Quantification of ecological flows

Following the identification of ecological flows, geomorphic units, controls, and timing of the flow, many tools, including mapping, data collection, and modeling will be needed to quantify the "conceptualized" streamflows identified earlier. Hydrodynamic models (Hardy, 1998; Rathburn and Wohl, 2003; Wheaton et al., 2004; Harby et al., 2007) and sediment entrainment methods and models (Reiser et al., 1989; Kondolf and Wilcock, 1996; Haschenburger and Wilcock, 2003; Rathburn and Wohl, 2003) may be used to examine hydro-geomorphic processes and scales of channel change. Two-dimensional hydrodynamic models have been proposed as adequate tools for representing complex hydraulics at pool-riffle and sediment patch scales (Wheaton et al., 2004; Brown and Pasternack, 2009). Sediment entrainment models based on boundary shear stress and critical shear stress calculations or stream power calculations have been proposed as practical tools to estimate the entrainment potential of sediment (Kondolf and Wilcock, 1996; Milan et al., 2001; Kondolf and Piegay, 2003; Caamano et al., 2009).

For the purpose of quantifying ecological flows, dealing with how to simulate geomorphic controls and how to validate the occurrence of an ecological flow can be a challenging task. In gravel-bed streams, distinction should be made between surface and subsurface structures and patterns. Buffington and Montgomery (1999) proposed a classification of textural patches with varying sediment sizes, Wilcock and Kenworthy (2002) distinguished between matrix-based sediment patches (loose structure) and framework-based sediment patches (matrix-based) depending on the percentage of fines in the sediment patch. Based on the percentage of fine sediment, Haschenburger and Wilcock (2003) identified immobile, partially mobile, and completely mobile sediment. Accordingly, quantifying streamflows to entrain specific sediment size or gradation from a specific habitat unit may demand extra caution and familiarity with literature on the complexity of gravel-bed streams.

Special attention should be paid to the selection of sediment entrainment methods and models. The selection should be based on the hydro-geomorphic process of concern, level of uncertainty, and objective of the study. Full mobility and partial mobility models for entraining sediment at different geomorphic scales are well established in the literature (Parker et al., 1982, Andrews, 1983; Buffington and Montgomery, 1997; Haschenburger and Wilcock, 2003; Pitlick et al., 2008), and the choice between them should be clear from the beginning in order to appropriately represent physical reality and minimize uncertainty. In a study that covered 80 years of the application of Shields parameter (θc), Buffington and Montgomery (1997) found that values of Shields parameter varied between 0.03 and 0.086. They argued that the selection of θc should depend on the study objectives and circumstances (Buffington and Montgomery,1997). Gordon et al. (2004), suggested values that range between 0.01 for very loose bed material to greater than 0.1 for imbricated bed material.


Phase 2: Validation of ecological flows

Following the quantification of the flows in Phase 1, it is necessary to confirm that these flows are part of the flow regime within the study area. Defining a flow regime could be facilitated using historic hydrological records in gauged streams. Or, calibrated hydrological models may be used to simulate the streamflow regime using a long-term meteorological record as input. A hydrological series of 12-20 years of flow data may be used to define and typify flow regime within a hydro-climatic zone (Petts, 2009). At this stage, conclusions on preliminary "real" linkages between hypothetical principles from the conceptual model and hydro-geomorphic and flow variability can be made.

Identifying the presence of a flow regime that is able to drive estimated or required hydro-geomorphic processes is one validation level. Another validation level is field observations of erosional and depositional features (i.e. direct calibration methods). Direct calibration methods are important techniques to verify the predictions of sediment entrainment models (Kondolf and Wilcock, 1996). A field protocol may be established within the feedback element process to monitor geomorphic controls such as sand content or pool depth during a study/project period following the suggestions of the conceptual model concerning what geomorphic controls to monitor and when (Figure 3). Geomorphic tools used within the direct calibration methods should take into consideration various factors such as the study area, representative habitat units, and differences between streambed structures (e.g. matrix vs. gravel framework) (Buffington et al., 1992; Bunte and Abt, 2001; Wilcock and Kenworthy, 2002).

Validation of habitat suitability should follow the premise of the Functional Habitat Concept (FHC) (Harper and Everard, 1998), landscape filters (Poff, 1997), and the ecological guild concept (Welcomme et al., 2006). These concepts treat habitat as a surrogate for biota, and generally assume that optimal habitat means optimal biodiversity. The conceptual model defines geomorphic habitat suitability by linking geomorphic variables to ecological needs related to channel morphology and substrate. As opposed to habitat simulation models which identify suitable habitat based on velocity and water depth metrics, "geomorphic habitat" suitability is not well defined in the literature. Therefore, uncertainties may be addressed in terms of the validation of geomorphic suitability before and after a certain flow event or dam release using direct calibration methods (Kondolf and Wilcock, 1996). Direct calibration methods verify expected relationships between flow and discharge-related geomorphic variables by monitoring geomorphic variables identified in the conceptual model. For appropriate validation, a monitoring program should be run during a specific study period that pertains to an ecological need, similar to approaches used for spawning rehabilitation projects (Wheaton et al., 2004), and spawning-related flow prescriptions (Escobar Arias and Pasternack, 2011).

In case of available expertise and time, assessing the response of aquatic organisms to potential ecological flows using assemblages count and population dynamics can also be used (e.g. Vadas and Orth, 2000). For example, field observations of geomorphic controls such as pool depth can be accompanied by biological studies of fish population dynamics in pools over time in order to verify the expected biological response to changes in geomorphic controls.


Phase 3: Management Scenarios

Within the feedback element process (Figure 6), suspended sediment load and bed load may be measured and/or sediment data from available sediment gauges may be analyzed (Newson, 2002; Kondolf and Piegay, 2003; Gordon et al., 2004). In case of the lack of sediment data, the impact of sediment supply can be evaluated by surrogate measures of fine sediment supply such as the V* index which estimates the residual pool volume covered by superficial sediment (Lisle and Hilton, 1992). The impact of local sediment supply should be included in the study of sediment regime as well. Techniques to estimate sediment supply from bank erosion include measuring bank shear strength and installing steel-rod pins in a stream bank segment and measuring the penetration length of the steel-rod pins during the study period (Zaimes et al., 2004).

Using Figure 6, water management options (e.g. dam release, management of water takings) are inferred based on the availability of streamflows (i.e. flow regime validation) to drive the hydro-geomorphic processes needed to maintain critical geomorphic variable in suitable ranges (e.g. depth of superficial sediment in pools). Sediment management options (e.g. stream restoration, land use practices) can be of use in cases where the required streamflow does not exist in the flow regime, cannot be released, or if it exists but the sediment supply is too high. A field program that comprises the application of hydraulic and geomorphic tools may verify if erosion occurs or not (i.e. direct calibration methods). If erosion occurs, the feedback element concludes that an ecological flow target is met. If not, an analysis of stream hydrology records and parameters can show if the streamflow needed is part of the existing flow regime.

If the flow required is part of the existing flow regime, studying the impact of sediment supply to the stream segment can be used to assess the severity of pool sedimentation. In case of high sedimentation such that the hydro-geomorphic processes of concern are not able to mobilize excessive sediment, sediment maintenance plans such as pool dredging may be needed. On the other hand, if the flow needed is not part of the existing flow regime, water management options such as dam releases could be examined. However, in case of limited water management options, the management strategy might incorporate sediment management plans. Further studies, such as sediment budgets may be needed to assess whether pool filling is related to local or large scale processes. For large scale effects such as urban development or accelerated hillslope processes, land use management activities could be incorporated in the management strategy.


Results and Discussion

The Conceptual Model: The Two Modes

This paper proposes a conceptual model and a feedback element. The conceptual model builds on ecological principles that are well established in the peer-reviewed literature and to a lesser extent in practice. Wheaton et al. (2004) argue that while restoration concepts and tools explain "what" to investigate and assess, there is an issue in "how" to use these concepts in an effective manner to provide guidance to restoration practitioners. The conceptual model proposes guidelines that are based on the understanding that articulating guidelines for integrating ecological requirements into environmental flow rules requires two eyes: the eye of the hydrologist and the eye of the ecologist. Accordingly, the conceptual model tries to integrate stream ecology and stream hydrology using two perspectives (i.e. modes). These modes represent the eye of the hydrologist (i.e. causal linkages mode) and the eye of the ecologist/fish biologist (i.e. ecological input mode) (Figures 1 and 3). The conceptual mode allows a two-tiered approach to integrating ecological input into streamflows with geomorphic function. Many restoration initiatives and studies use causal linkages as a standalone approach, and assume that ecological requirements are inherently evident. However, ignoring the bottom-up understanding inhibits concise analysis of the overall stream system (Poole, 2002; Dollar et al., 2007) and results in providing ineffective tools for stream restoration (Newson, 2002; Lake et al., 2007; Wilcock, 2012).

The conceptual model proposed in this paper does not have the intention or the knowledge to include all hydro-geomorphic and ecological processes that take place in gravel-bed streams. One of the justifications is that many hydro-geomorphic processes are not fully understood (Buffington, 2012; Wilcock, 2012). These processes include scales of channel changes such as changes in channel boundaries and grain-scale adjustments (Buffington, 2012). Another justification behind the simplicity of the conceptual model is that numerous hypotheses concerning erosion and deposition processes exist in the literature. For example, the pool-riffle maintenance mechanism is one of the most debated processes in gravel-bed streams. Hypotheses that explain pool-riffle maintenance include the velocity reversal hypothesis and its variations (Keller, 1971; Keller, 1978; Wilkinson et al., 2004; Caamano et al., 2009) and the secondary flow structures hypothesis (Thompson and Wohl, 2009). Since the velocity reversal hypothesis has been rigorously tested in the literature and since consensus is not often expected in fluvial geomorphology because it is not exact science (Wilcock, 2012), the hypothesis is used in the conceptual model as the chief mechanism responsible for the bed form scale change (pool-riffle mesohabitat scale). Moreover, the velocity reversal hypothesis is relevant to many ecological processes and functions, whereby the integration of both concepts is rendered process-based, science-based, and practical.

It is commonplace in conceptual models to highlight processes at the expense of other processes, or exclude variables in order to simplify linkages or effort. One of the most implemented conceptual models in environmental flow studies is PHABSIM (Bovee, 1982; Milhous et al., 1989; Stalnaker et al., 1995). Petts (2009) notes that despite the scientific weaknesses of PHABSIM pointed out in the literature, the conceptual simplicity of the tool has made it popular worldwide and motivated new and progressive research on ecological linkages and habitat needs. This does not imply that there are weaknesses in the conceptual model proposed in this paper, but indicates the nature of its overarching objective and assumptions taking into consideration that while it is science-based it is neither a standalone approach nor a deterministic model for assessing ecological and hydro-geomorphic processes.


Ecological Input for Identifying Ecological Flows

The functional habitat component of the conceptual model (Steps 1 and 2) calls for defining ecological guilds and geomorphic controls before embarking upon prescribing environmental flow rules. This approach has the potential of prioritizing stream habitat conservation in general and environmental flow rules in specific, by focusing on critical habitat units for predominant ecological guilds and the geomorphic controls on them spatially and temporarily. Dividing a watershed or a stream segment into habitat units and allocating predominant ecological guilds and geomorphic controls at each habitat unit (Figure 4) could provide restoration ecologists and water managers with a valuable guidance. The ecological guild concept is not foreign to stream management practices. Karr (1981) used trophic guild and other guilds as indicators of the ecological state of a river or a stream through the Index of Biological Integrity (IBI) which is a management tool used in North America in order to assess water quality issues in streams. Classifying aquatic species into dominant ecological guilds and identifying physical controls at different habitat scales have been recently applied for assessing habitat quality in European rivers to meet the requirements of the Water Framework Directive (Welcomme et al, 2006; Noble et al., 2007). Welcomme et al. (2006) proposed a framework that divided a watershed into two upland stream guilds, three lentic lowland guilds and four lowland lotic guilds. For each region, specific dominant guilds that favored specific physical attributes were chosen for conservation. Since stream conservation tools that use ecological guilds already exist in practice, it is anticipated that restoration practitioners and freshwater biologists will find the conceptual model presented in this paper effective and feasible for implementation.

As opposed to studying ecological needs based on taxonomic classifications, this study investigates ecological needs in terms of ecological guilds because the evaluation of biological requirements of aquatic organisms from the perspective of guilds can provide more information about ecological functions (Austen et al., 1994; Noble et al., 2007), provide functional linkages to physical variables in streams and rivers (Welcomme et al., 2006; Lasne et al., 2007), and introduce predictive tools to the science of stream restoration (Poff, 1997; Harper and Everard, 1998; Storey and Lynas, 2007). Use of the ecological guild concept can indicate potential biotic response to changes in physical processes associated with streamflows (Welcomme et al., 2006). Another advantage of using guilds, rather than indicator species, is that ecological functions and needs for several species can be better established (Austen et al.. 1994; Poff et al., 2006; Noble et al., 2007).


Quantifying Ecological Flows

The quantification of the ecological flows identified in the conceptual model may seem like a straightforward task. This concept may be supported by the presence of countless tools and models to estimate flows in streams and rivers. However, the use of state of the art tools does not always guarantee success (Hardy, 1998; Wheaton et al., 2004; Petts, 2009). This paper provides general recommendations concerning aspects that are often neglected while estimating hydro-geomorphic processes for habitat maintenance. For example, while the median particle size (D50) may be used as the representative sediment particle size to entrain from pools to erode superficial excess sediment from pools, it may not be the appropriate size to entrain from riffles for flushing fine sediment to provide for the reproductive guild. As a result, the streamflows determined for both purposes may be different, constituting a range of flows rather than one single flow (Figure 5). The understanding of textural patches according to Buffington and Montgomery (1997) and the understanding of patches as loose and framework-based according to Wilcock and Kenworthy (2002) may provide a valuable tool to assess and map substrate structure before embarking upon estimating required streamflows.

It should be noted that the recommendation of specific tools for the quantification of ecological flows is not one of the objectives of the conceptual framework. The feedback element is structured as a process, and it is the process that is intended to be followed within the bigger conceptual framework (Figure 6), and not the fine details. This premise coincides with the overall objective of the feedback element, which is to test the conceptual model and contribute to proposing management decisions under the pretext of the conceptual framework. Moreover, keeping the feedback element as a dynamic process that is adaptive and inclusive may render it transferrable to different hydrological, ecological and geomorphic contexts.


Water Management vs. Sediment Management

Streamflow management decisions are generally influenced by processes that are spatially and temporally larger than those occurring at habitat scales (Newson and Newson, 2000; Newson, 2002; Dollar et al., 2007). A key process from that category is sediment regime, which needs to be examined at the watershed scale and within the historical context (Newson, 2002). The investigation of both water and sediment regimes within the feedback element component of the conceptual framework (Figure 6) is important in order to define critical pathways between geomorphic controls discussed in the conceptual model and the drivers behind them. Many researchers have shown that combined impacts of flow alteration and land uses have led to alteration and degradation of channel morphology and instream habitats (Niezgoda and Johnson, 2005; Beechie et al., 2009). Differentiating between streamflow management options and other management options (e.g. sediment management) is very important (Souchon et al., 2008; Beechie et al., 2009). If the changes are due to multiple stressors on the entire watershed, the chance of maintaining habitat structure by only manipulating flows is small (Souchon et al., 2008).

Examples from the literature that could support the process proposed in Figure 6 include a study of streamflows to maintain pool depth for the Trinity River in California. Wilcock et al. (1996) suggested dredging pools as a sediment management option because streamflows proposed to entrain fine sediment from diminished pools were high enough to degrade the whole morphology of the channel. Streams experiencing channel narrowing and incision due to reduced coarse sediment supply from the watershed provide another example related to riffle micro- and mesohabitats maintenance. Researchers proposed gravel augmentation projects in order to maintain substrate suitability for riffle microhabitat (Wheaton et al., 2004; Brown and Pasternack, 2009), since streamflow manipulation would not be able to maintain gravel supply from upstream when gravel is missing from sediment supply.


Uncertainty Considerations

While developing the conceptual framework, our aim was not to develop a comprehensive, integrated conceptual model that takes into account uncertainties in spatial and temporal variation, but rather to provide a practical guidance on integrating ecological input into ecological flows with geomorphic functions. However, the conceptual framework ''embraces'' the concept of uncertainty as an integral part of the science of stream restoration (Sear et al., 2008; Wheaton et al., 2008; Wilcock, 2012). The conceptual model developed in this study is based on concepts and tools that are well established in the peer-reviewed literature. Since detailed understanding and deterministic models of ecological functions and processes (Arthington et al., 2006; Petts, 2009) and hydro-geomorphic processes (Wheaton et al., 2008; Buffington, 2012; Wilcock, 2012) are not available, identifying and communicating uncertainty may be facilitated during the feedback element process, which is meant to test the hypotheses presented in the conceptual model and provide a feedback loop as the name implies. More specifically, it is anticipated that discussions are held amongst practitioners in regard to field protocols of interest, the hydrodynamic models needed to delineate habitat, and field measurements including sedimentary and flow-related measurements. The conceptual model and its structure and assumptions are presumed to be the preliminary reference for this kind of discussion, and the overall conceptual framework (Figure 6) is suggested as a process where uncertainties are communicated within a system-based approach.



Integrating ecological input into environmental flow rules has always been a challenging task (Kondolf and Wilcock, 1996; Gordon et al., 2004; Bunn and Arthington, 2002; Arthington et al., 2006; Dollar et al., 2007; Poff et al., 2009; Lapointe, 2012). Despite well-established tools and concepts that link fluvial geomorphology to stream ecology, restoration practitioners and water managers lack effective and practical guidelines on appropriate habitat variables, geomorphic controls, and spatial and temporal scales to determine environmental flows with geomorphic functions. The conceptual framework proposed in this study may present a feasible and effective approach to address this gap.

The feedback element provides an approach to examine the occurrence of ecological flow identified in the conceptual model, and propose water and/or sediment management decisions. The feedback element is a flexible and dynamic process that demands creativity, communication amongst practitioners and scientists, and adaptivity within the process. Since detailed and exact understanding of ecological processes and hydro-geomorphic processes is not available in literature and practice (Arthington et al., 2006; Poff et al., 2009; Wilcock, 2012), the feedback element provides means to adaptive management of environmental flow rules.

This paper does not intend to present an exhaustive review of hydro-geomorphic processes at a watershed scale or specific scales beyond pool-riffle morphology, nor do we attempt to present the optimal scheme for prescribing environmental flows or obtaining an ecological input for environmental flow prescriptions. Rather, our approach is a minimalistic one that uses practical and most recent concepts and tools in stream hydrology, fluvial geomorphology, and stream ecology, without compromising the science behind those tools and concepts, thereby producing a process-based framework and guidance that is more likely to be used.



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