Ecohydraulics -- Contents -- List of Contributors -- 1 Ecohydraulics: An Introduction -- 1.1 Introduction -- 1.2 The emergence of ecohydraulics -- 1.3 Scope and organisation of this book -- References -- I Methods and Approaches -- 2 Incorporating Hydrodynamics into Ecohydraulics: The Role of Turbulence in the Swimming Performance and Habitat Selection of Stream-Dwelling Fish -- 2.1 Introduction -- 2.1.1 'Standard' ecohydraulic variables -- 2.2 Turbulence: theory, structure and measurement -- 2.2.1 Statistical descriptions of turbulence -- 2.2.2 Coherent flow structures -- 2.2.3 Measuring turbulence in the field -- 2.3 The role of turbulence in the swimming performance and habitat selection of river-dwelling fish -- 2.3.1 Swimming performance -- 2.3.2 Habitat selection -- 2.4 Conclusions -- Acknowledgements -- References -- 3 Hydraulic Modelling Approaches for Ecohydraulic Studies: 3D, 2D, 1D and Non-Numerical Models -- 3.1 Introduction -- 3.2 Types of hydraulic modelling -- 3.3 Elements of numerical hydrodynamic modelling -- 3.3.1 Mathematical model -- 3.3.2 Discretization methods -- 3.3.3 Mesh -- 3.3.4 Mesh quality -- 3.3.5 Boundary conditions -- 3.3.6 Initial conditions -- 3.3.7 Model parameters -- 3.3.8 Model parameterization -- 3.3.9 Validation -- 3.3.10 Scaling and averaging -- 3.4 3D modelling -- 3.4.1 Model setup -- 3.5 2D models -- 3.5.1 Model setup -- 3.6 1D models -- 3.6.1 1D model setup -- 3.7 River floodplain interaction -- 3.8 Non-numerical hydraulic modelling -- 3.9 Case studies -- 3.9.1 1D modelling of the Kootenai River, Idaho, USA -- 3.9.2 Pseudo-2D modelling of the Biobío River, Chile -- 3.9.3 2D modelling of the Saane River, Switzerland -- 3.9.4 3D modelling of salmon redds -- 3.10 Conclusions -- Acknowledgements -- References -- 4 The Habitat Modelling System CASiMiR: A Multivariate Fuzzy Approach and its Applications.

4.1 Introduction -- 4.1.1 Background -- 4.1.2 Physical habitat modelling in general -- 4.1.3 Fuzzy logic in ecohydraulic modelling -- 4.2 Theoretical basics of the habitat simulation tool CASiMiR -- 4.2.1 Background and development -- 4.2.2 Functional principle of CASiMiR -- 4.2.3 Calibration of the fuzzy approach -- 4.2.4 Advantages and limitations of the fuzzy approach -- 4.3 Comparison of habitat modelling using the multivariate fuzzy approach and univariate preference functions -- 4.3.1 Biota-physical relations: fuzzy approach versus preference functions -- 4.3.2 Case study: River Aare, Switzerland - simulation of spawning habitats for grayling with the fuzzy approach and preference functions -- 4.4 Simulation of spawning habitats considering morphodynamic processes -- 4.4.1 Ecological relevance of morphodynamic processes -- 4.4.2 Concept of implementing morphodynamic processes in CASiMiR -- 4.4.3 Case study: River Mur, Austria - morphodynamic processes and gravel-spawning fish habitat -- 4.5 Habitat modelling on meso- to basin-scale -- 4.5.1 Requirements of habitat assessment on larger scales -- 4.5.2 Concept of evaluation of mesohabitats using MesoCASiMiR -- 4.5.3 Case study: River Neckar, Germany - habitat fragmentation and connectivity -- 4.6 Discussion and conclusions -- References -- 5 Data-Driven Fuzzy Habitat Models: Impact of Performance Criteria and Opportunities for Ecohydraulics -- 5.1 Challenges for species distribution models -- 5.1.1 Knowledge-based versus data-driven models -- 5.1.2 Ecological boundaries -- 5.1.3 Interdependence of variables -- 5.1.4 The knowledge acquisition bottleneck -- 5.1.5 Data-driven knowledge acquisition -- 5.2 Fuzzy modelling -- 5.2.1 Fuzzy rule-based modelling -- 5.2.2 Fuzzy rule base optimisation -- 5.3 Case study -- 5.3.1 Study area and collected data.

5.3.2 Fuzzy rule-based modelling and rule base training -- 5.3.3 Model application -- 5.3.4 Results -- 5.3.5 Discussion -- References -- 6 Applications of the MesoHABSIM Simulation Model -- 6.1 Introduction -- 6.2 Model summary -- 6.2.1 Identifying biological targets and indicators -- 6.2.2 Establishing habitat suitability criteria -- 6.2.3 Mapping and evaluation of instream habitat -- 6.2.4 Habitat survey -- 6.2.5 Upscaling -- 6.2.6 Adjusting biophysical templates to reflect reference habitat -- 6.2.7 Reference flow time series -- 6.2.8 Habitat time series analysis -- 6.2.9 Scenario comparison -- 6.2.10 Interpretation and application -- Acknowledgements -- References -- 7 The Role of Geomorphology and Hydrology in Determining Spatial-Scale Units for Ecohydraulics -- 7.1 Introduction -- 7.2 Continuum and dis-continuum views of stream networks -- 7.3 Evolution of the geomorphic scale hierarchy -- 7.3.1 Origins -- 7.3.2 Adoption, adaptation and application -- 7.3.3 Difficulties -- 7.4 Defining scale units -- 7.4.1 Meso scale -- 7.4.2 Reach scale -- 7.4.3 Segment scale -- 7.5 Advancing the scale hierarchy: future research priorities -- References -- 8 Developing Realistic Fish Passage Criteria: An Ecohydraulics Approach -- 8.1 Introduction -- 8.2 Developing fish passage criteria -- 8.2.1 The traditional approach -- 8.2.2 Criticisms of the traditional approach -- 8.2.3 The ecohydraulic approach -- 8.3 Conclusions -- 8.4 Future challenges -- References -- II Species-Habitat Interactions -- 9 Habitat Use and Selection by Brown Trout in Streams -- 9.1 Introduction -- 9.2 Observation methods and bias -- 9.3 Habitat -- 9.4 Abiotic and biotic factors -- 9.5 Key hydraulic factors -- 9.6 Habitat selection -- 9.7 Temporal variability: light and flows -- 9.7.1 Case study: varying water flows and habitat use -- 9.8 Energetic and biomass models.

9.9 The hyporheic zone -- 9.10 Spatial and temporal complexity of redd microhabitat -- 9.11 Summary and ways forward -- References -- 10 Salmonid Habitats in Riverine Winter Conditions with Ice -- 10.1 Introduction -- 10.2 Ice processes in running waters -- 10.3 Salmonids in winter ice conditions -- 10.3.1 Acclimatization in winter -- 10.3.2 Winter habitat criteria -- 10.4 Summary and ways forward -- References -- 11 Stream Habitat Associations of the Foothill Yellow-Legged Frog ( Rana boylii): The Importance of Habitat Heterogeneity -- 11.1 Introduction -- 11.2 Methods for quantifying stream habitat -- 11.2.1 Study area -- 11.2.2 Rana boylii sampling -- 11.2.3 Habitat associations -- 11.2.4 Statistical analyses -- 11.3 Observed relationships between R. boylii and stream habitat -- 11.3.1 Mesohabitat associations in Shady Creek -- 11.3.2 Mesohabitat associations on other study creeks -- 11.3.3 Reach-scale habitat associations -- 11.4 Discussion -- 11.4.1 Mesohabitat associations -- 11.4.2 Reach-scale associations -- 11.4.3 Habitat heterogeneity -- References -- 12 Testing the Relationship Between Surface Flow Types and Benthic Macroinvertebrates -- 12.1 Background -- 12.2 Ecohydraulic relationships between habitat and biota -- 12.3 Case study -- 12.3.1 Site details and method -- 12.3.2 Results -- 12.4 Discussion -- 12.5 Wider implications -- 12.6 Conclusion -- References -- 13 The Impact of Altered Flow Regime on Periphyton -- 13.1 Introduction -- 13.2 Modified flow regimes -- 13.3 The impact of altered flow regime on periphyton -- 13.3.1 Species composition and abundance -- 13.3.2 Biomass -- 13.3.3 Periphyton proliferations -- 13.4 Case studies from Slovenia -- 13.4.1 The Sava Dolinka River -- 13.5 Conclusions -- References -- 14 Ecohydraulics and Aquatic Macrophytes: Assessing the Relationship in River Floodplains -- 14.1 Introduction.

14.2 Macrophytes -- 14.3 Life forms of macrophytes in running waters -- 14.4 Application of ecohydraulics for management: a case study on the Danube River and its floodplain -- 14.4.1 Study site -- 14.4.2 Sampling -- 14.4.3 Data analysis -- 14.4.4 Ecohydraulic habitat-macrophyte relationship -- 14.4.5 Water depth - an ecohydraulic requirement for macrophytes -- 14.5 Conclusion -- Acknowledgements -- References -- 15 Multi-Scale Macrophyte Responses to Hydrodynamic Stress and Disturbances: Adaptive Strategies and Biodiversity Patterns -- 15.1 Introduction -- 15.2 Individual and patch-scale response to hydrodynamic stress and disturbances -- 15.2.1 Response traits to hydrodynamic forces -- 15.2.2 Indirect effects of flow on macrophytes -- 15.3 Community responses to temporary peaks of flow and current velocity -- 15.3.1 Highly disturbed communities -- 15.3.2 Intermediately disturbed communities -- 15.4 Macrophyte abundance, biodiversity and succession -- 15.4.1 Lotic ecosystems -- 15.4.2 Flood-disturbed ecosystems -- 15.5 Conclusion -- References -- III Management Application Case Studies -- 16 Application of Real-Time Management for Environmental Flow Regimes -- 16.1 Introduction -- 16.2 Real-time management -- 16.3 The setting -- 16.4 The context and challenges with present water allocation strategies -- 16.5 The issues concerning the implementation of environmental flow regimes -- 16.6 Underlying science for environmental flows in the Klamath River -- 16.6.1 Hydrology-based flow regimes -- 16.6.2 Habitat time series-based flow regimes -- 16.6.3 Flow-and-habitat-based integration for recommended flow regimes -- 16.6.4 Peer review of Hardy et al. (2006a) -- 16.7 The Water Resource Integrated Modelling System for The Klamath Basin Restoration Agreement -- 16.8 The solution - real-time management -- 16.9 Example RTM implementation.

16.10 RTM performance.