Durham E-Theses Evaluating the eectiveness of restoring longitudinal connectivity for sh migration and dispersal in impacted river systems TUMMERS, JEROEN,STEVEN How to cite: TUMMERS, JEROEN,STEVEN (2016) Evaluating the eectiveness of restoring longitudinal connectivity for sh migration and dispersal in impacted river systems, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/11924/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk 2 Evaluating the effectiveness of restoring longitudinal connectivity for fish migration and dispersal in impacted river systems Submitted for the degree of Doctor of Philosophy at the University of Durham by Jeroen Steven Tummers Department of Biosciences Durham University 2016 Evaluating the effectiveness of restoring longitudinal connectivity for fish migration and dispersal in impacted river systems Abstract In this study, the impact of anthropogenic in-stream structures on migration and dispersal of a variety of fish species was investigated. The effectiveness of attempted restoration of longitudinal connectivity in fragmented stream and river systems, through implementation of various fish pass designs, both technical and nature oriented, was evaluated for fish of varying age classes. The outcomes of this research are of importance for river management schemes that aim to restore degraded freshwater systems bound by legislation from the EU Water Framework Directive, which requires good connectivity and habitat quality within freshwater systems. Fish community composition in relation to effects of in-stream structures and habitat conditions was investigated on three degraded stream networks, so that future opportunities for longitudinal connectivity restoration could be identified. Differences in fish community composition above and below common types of structures were determined, whereby species richness and density per species showed greatest differences for flow manipulating culvert structures, especially pipe culverts. Obstacle effects on fish dispersal and migration, and the effectiveness of connectivity restoration - obstacle removal and design of various types of fish passes - on those same obstacles were evaluated using a variety of approaches. These included capture-mark-recapture of different life stages of a weak swimmer (European bullhead Cottus perifretum) and of a strong swimmer (brown trout Salmo trutta) tagged with passive integrated transponder (PIT) and/or visible implant elastomer (VIE), displacement studies of juvenile trout and radio telemetry of adult freshwater-resident and sea-going morphotypes of brown trout. Longitudinal connectivity for fish was shown to have improved post-restoration, exemplified by improved fish passage over the multiple structures in both directions, while permeability of unrestored structures remained low. The efficacy of a technical Larinier super active baffle fish pass, a widespread design in Europe, was assessed for upstream-migrating adult river lamprey. Situated next to a common Crump weir, the pass was designed to facilitate passage for a wide range of fish species. Over two migration seasons, with a variety of flow levels occurring in both, the pass was tested for efficacy before and after modification with studded tiles mounted on the inside wall. By using fixed PIT arrays, poor passage through the fish pass by river lamprey was shown before modification, and improved marginally post- modification. Acoustic telemetry identified direct passage over the weir to be two-fold higher than through the modified fish pass. In the context of the Water Framework Directive, there is a strong need to develop well- grounded fish passage criteria, not only for fish species with strong swimming capacity, but for a wide range of fish species and life stages. Ideally, all types of fishways should be critically assessed, in situ, to allow river managers to make more informed decisions on restoring fragmented stream systems. ii Index Index iii List of figures vii List of tables xii Declaration xvii Acknowledgements xviii Chapter 1: The importance of river connectivity for freshwater fishes 21 1.1 General introduction 22 1.2 Migratory behaviour of fishes 23 1.3 Threats to conservation of freshwater fish species 29 1.3.1 Anthropogenic in-stream structures 31 1.4 The EU Water Framework Directive 36 1.4.1 Aims and approach 36 1.4.2 Surface water quality status 39 1.5 Restoring river connectivity 40 1.5.1 Removal of in-stream obstacles to movement 41 1.5.2 Fishways to reduce river fragmentation 42 1.5.2.1 History and distribution 44 1.5.2.2 Technical fishways 45 1.5.2.3 Specialist fish passes 50 1.5.2.4 Fish lifts and fish locks 52 1.5.2.5 Nature-like solutions 55 1.5.2.6 Solutions facilitating downstream passage 58 1.5.2.7 Evaluation of fishway efficiency 61 1.5.3 Consequences of fish passage often overseen 66 1.5.3.1 Ecological traps 67 1.5.3.2 Fallback 67 1.5.3.3 Selective passage 68 1.5.3.4 Species introduction 70 1.6 Aims of thesis 70 iii Chapter 2: Examining the effects of in-stream engineered structures and environmental variables on fish community composition in fragmented stream networks 72 2.1 Introduction 73 2.2 Methods 80 2.2.1 Study area 80 2.2.2 Types of survey sites and habitat conditions 87 2.2.3 Sampling procedure for fish assemblages 92 2.2.4 Habitat, environmental conditions and macroinvertebrates 93 2.2.5 Data analysis and statistical approach 95 2.3 Results 99 2.3.1 Classification of sites 99 2.3.2 Fish communities 110 2.3.2.1 Fish species distribution and density 110 2.3.2.2 Habitat conditions explaining species presence 114 2.3.2.3 Obstacle effects on fish species densities 118 2.3.2.4 Fish species composition similarity between tributaries and distance between sites 123 2.3.2.5 Impacts of multiple obstacle types on fish community composition 127 2.4 Discussion 128 2.4.1 Differences in fish community between stream networks 128 2.4.2 Obstacle effects on fish communities 129 2.4.3 Distance from main river and multiple obstacles in relation to fish density 132 2.4.4 Combined effects of habitat conditions, pollution and fragmentation 134 2.4.5 Connectivity restoration in the context of the Water Framework Directive 138 Chapter 3: Evaluating the effectiveness of restoring longitudinal connectivity for stream fish communities: towards a more holistic approach 140 3.1 Introduction 141 3.2 Methods 144 3.2.1 Study site 144 3.2.2 Study design 153 3.2.3 Habitat, environmental conditions and macroinvertebrates 153 3.2.4 Fish assemblages and densities 154 iv 3.2.5 Capture-mark-recapture surveys of dispersal and passage 155 3.2.6 Upstream passage efficacy of homing juvenile trout 158 3.2.7 Radio telemetry of trout during the spawning migration 159 3.2.8 Statistical approach and modelling 161 3.3 Results 166 3.3.1 Habitat characteristics 166 3.3.2 Fish assemblages, densities and recolonization 170 3.3.3 Capture-mark-recapture surveys of dispersal and passage 172 3.3.4 Upstream passage efficiency of homing juvenile trout 186 3.3.5 Radio telemetry of trout during the spawning migration 187 3.4 Discussion 190 3.4.1 Habitat fragmentation effects on fish communities and density 191 3.4.2 Fish dispersal behaviour, recolonization and survival 194 3.4.3 Barrier permeability and fishway efficiency 198 3.4.4 Upstream migration by adult trout 201 3.4.5 Conclusion and recommendations 202 Chapter 4: Evaluating the effectiveness of a Larinier super active baffle fish pass for European river lamprey Lampetra fluviatilis before and after modification with wall-mounted studded tiles 203 4.1 Introduction 204 4.2 Methods 207 4.2.1 Study site 207 4.2.2 Characteristics of the fish passes 209 4.2.3 Lamprey capture and tagging 213 4.2.4 Telemetry 216 4.2.5 Environmental conditions and statistical analysis 220 4.3 Results 221 4.3.1 Hydrological conditions 221 4.3.2 Fish pass efficiency and time taken to locate the pass entrance 223 4.3.3 Fish pass ascent attempts and environmental effects 225 4.3.4 Variance in passage attempts grouped by release date 231 4.3.5 Migration delay and diel activity 231 4.3.6 Acoustic telemetry of lamprey approaching the weir 233 4.4 Discussion 235 v 4.4.1 Effect of flow velocity on passage success 236 4.4.2 Effects of baffles and turbulence on passage success 237 4.4.3 Factors influencing migration activity of river lamprey 238 4.4.4 Routes of passage 240 4.4.5 Consequences of unsuccessful passage 240 4.4.6 Effects of modification of the SAB fish pass and alternative solutions 242 Chapter 5: General discussion 245 5.1 Summary of outcomes in relation to aims 246 5.2 Justification and limitations of methodologies used 249 5.3 Implications for river management and future research 258 Appendix I: Supplementary material for Chapter 2/3 266 Water body labels River Wear 266 Water body labels Brancepeth Beck, River Browney, Old Durham Beck and River Deerness 266 Appendix II: Supplementary material for Chapter 3 267 Hydromorphology in vicinity of Deerness structures 267 Evaluating the effectiveness of restoring longitudinal connectivity for stream fish communities: towards a more holistic approach 278 Appendix III: Supplementary material for Chapter 4 289 Evaluating the effectiveness of a Larinier super active baffle fish pass for European river lamprey Lampetra fluviatilis before and after modification with wall-mounted studded tiles 289 Literature cited 301 vi List of figures Figure 1.1: Types of migration between three functional habitats: feeding, spawning and refuge.