Note: Intro -- In Memoriam: John Quinn, PhD, August 5, 1957-November 13, 2018 -- Foreword -- Preface -- Acknowledgements -- Contents -- Editors and Contributors -- Chapter 1: Context for Restoration -- 1.1 Introduction -- 1.2 History of Lake Research in New Zealand -- 1.3 Policy Framework for Lake Management and Restoration in New Zealand -- 1.4 International Context -- 1.5 Introduction to Chapters -- References -- Chapter 2: Modelling for Catchment Management -- 2.1 Introduction -- 2.2 The Purpose and Types of Catchment Models -- 2.2.1 The Purpose of Catchment Modelling -- 2.2.2 Types of Catchment Models -- 2.3 Detailed Descriptions of the Different Types of Catchment Models -- 2.3.1 Statistically Based Catchment Models -- 2.3.2 Process-Based Catchment Models -- 2.3.3 Hybrid Catchment Models -- 2.3.4 Regression-Based Versus Process-Based Catchment Models -- 2.4 Choosing and Evaluating the Right Model -- 2.4.1 Choosing the Right Model or Combination of Models -- 2.4.2 Evaluation of Catchment Models -- 2.4.3 The Need for Guidelines on How to Use the Model Selected -- 2.5 Catchment Modelling in New Zealand -- 2.5.1 Historical Context -- 2.5.2 Brief Summary of Catchment Models Commonly Used in New Zealand -- 2.5.2.1 GLEAMS -- 2.5.2.2 ROTAN -- 2.5.2.3 AquiferSim -- 2.5.2.4 OVERSEER -- 2.5.2.5 SPASMO -- 2.5.2.6 SPARROW -- 2.5.2.7 CLUES -- 2.5.2.8 SWAT -- 2.5.2.9 DHI MIKE -- 2.5.2.10 Delft3D -- 2.5.2.11 Hydroepidemiological Catchment Models -- 2.5.2.12 Nitrate and Phosphorus Leaching Maps -- 2.5.3 Availability of Model Formulation, Algorithms, and Source Code -- 2.5.4 Models for Compliance or Regulatory Purposes -- 2.5.5 A Small Catchment Context. A CLUES Example -- 2.5.6 A Large Catchment Context. A GLEAMS Example -- 2.6 Catchment Modelling in a Large Basin Outside of New Zealand: A SPARROW Example. , 2.7 Use of Catchment Model Output for Lake and Reservoir Modelling -- 2.8 Benefits of Integrated Monitoring and Modelling -- References -- Chapter 3: Modelling Water Quality to Support Lake Restoration -- 3.1 Introduction to Lake Models -- 3.2 Types of Models -- 3.2.1 Empirical Models -- 3.2.2 Neural Networks -- 3.2.3 Deterministic models -- 3.3 Selecting an Appropriate Model -- 3.4 Model Performance Criteria and Skill Assessment -- 3.5 Data Assimilation for Modelling -- 3.6 Synthesising Ecological Model Applications: The Importance of Calibration -- 3.7 Introduction to New Zealand Lake Model Applications -- 3.8 New Zealand Examples -- 3.8.1 Modelling to Inform Potential for Regime Shifts and Macrophyte Collapse in Waituna Lagoon, Southland -- 3.8.2 Modelling to Support an Engineered Inflow Diversion for Restoration of Water Quality in Lake Rotoiti -- 3.8.3 Modelling of Pest Fish and Catchment Effects on Lake Water Quality -- 3.8.4 Wastewater Dispersion Modelling in Lake Rotorua -- 3.9 Future Prospects -- References -- Chapter 4: Agricultural Catchment Restoration -- 4.1 Introduction -- 4.2 Sources of Contaminants -- 4.3 Pathways of Contaminant Loss -- 4.4 Mitigation Strategies -- 4.4.1 Implementing Mitigations to Decrease Catchment-Scale Losses -- 4.5 Conclusions and Future Prospects -- References -- Chapter 5: Nutrient Budgets in Lakes -- 5.1 Sources and Fates of Nutrients in Lakes -- 5.1.1 The Nutrient Mass Balance -- 5.1.2 Sources of Nutrients -- 5.1.2.1 Stream Inflows -- 5.1.2.2 Groundwater Inputs -- 5.1.2.3 Atmospheric Inputs -- 5.1.3 Internal Sources of Nutrients to the Water Column -- 5.1.3.1 Geochemistry Effects on Nutrient Release From the Sediment -- 5.1.3.2 Accumulation of Dissolved P in Hypolimnia -- 5.1.3.3 pH-Dependent P Release -- 5.1.3.4 Sediment N Release -- 5.1.3.5 Wind-Induced Nutrient Resuspension -- 5.1.3.6 N-Fixation. , 5.1.4 Fates of Nutrients in Lakes -- 5.1.4.1 Sequestration of N and P, and Conversion of Bioavailable Forms of N to N2 -- 5.1.4.2 Estimation of the Phosphorus Retention Coefficient -- 5.1.4.3 Estimation of the Nitrogen Retention Coefficient -- 5.1.4.4 Flushing and Seepage -- 5.2 Flipping Lakes -- 5.3 Nutrients Contained in Biota: Fish, Macrophytes, and Phytoplankton -- 5.4 Lake Restoration by Adjusting Components of the Nutrient Budget -- 5.5 Estimating Nutrient Concentrations and Internal Loading Using Empirical Models -- 5.5.1 Estimating Nutrient Concentrations Using Empirical Models -- 5.5.2 Net Versus Gross Internal Loading -- 5.5.3 Estimating the Net Internal Nutrient Load -- 5.5.4 Estimating Gross Internal Loading -- 5.5.5 Uncertainty in Mass-Balance Estimates -- 5.6 Future Prospects -- References -- Chapter 6: Physical Processes for In-Lake Restoration: Destratification and Mixing -- 6.1 Introduction -- 6.1.1 Thermal Stratification -- 6.1.2 Consequences of Thermal Stratification -- 6.1.2.1 Deoxygenation -- 6.1.2.2 Nutrient Release -- 6.1.2.3 Light Penetration -- 6.2 Lake Mixing -- 6.2.1 Natural Processes -- 6.2.2 Artificial Processes -- 6.2.3 Influence of Lake Size and Shape -- 6.2.4 Destratification and Aeration Mechanisms -- 6.2.4.1 Bubble-Plume Diffuser -- 6.2.4.2 Bubble-Plume Diffuser in a Non-stratified Water Body -- 6.2.4.3 Bubble-Plume Diffuser in a Stratified Water Body -- 6.2.5 Morphology and Timing -- 6.2.6 Aeration Protocols -- 6.3 Mechanical Mechanisms -- 6.3.1 Solar-Powered Water Mixers -- 6.3.2 Constrained Bubble Plumes -- 6.4 Selective Draw-Induced Stratification -- 6.4.1 Case Study: Upper Huia Reservoir -- 6.5 Oxygenation of the Hypolimnion Without Mixing -- 6.6 Down-Flow Mixing Devices -- 6.7 Computer Modelling -- 6.8 Aeration Case Studies -- 6.8.1 Opuha Dam -- 6.8.1.1 Background -- 6.8.1.2 Water Quality Problems. , 6.8.1.3 Design Issues -- 6.8.1.4 Mitigation Measures -- 6.8.2 Virginia Lake -- 6.8.2.1 Background -- 6.8.2.2 Water Quality Problems -- 6.8.2.3 Design Issues and Mitigation Measures -- 6.9 Future Developments -- References -- Chapter 7: Flocculants and Sediment Capping for Phosphorus Management -- 7.1 Introduction -- 7.1.1 Nutrient Limitation of Phytoplankton -- 7.1.2 Sources of Nutrients in Freshwater Lakes and Reservoirs -- 7.1.3 Internal Nutrient Cycling -- 7.1.4 Definitions -- 7.2 Flocculation -- 7.3 Sediment Capping -- 7.3.1 Passive Sediment Capping Agents -- 7.3.2 Active Sediment Capping Agents -- 7.3.3 Specific P-Inactivation Agents -- 7.3.3.1 Allophane -- 7.3.3.2 Iron -- 7.3.3.3 Alum -- 7.3.4 Surface Application Issue -- 7.3.5 Does Brief Exceedance of the Permitted Maximum Have an Effect? -- 7.3.6 Aqual-P -- 7.3.7 Phoslock -- 7.3.8 Calcite -- 7.4 pH Effects and Speciation -- 7.4.1 Causes of High pH -- 7.4.2 Timing -- 7.5 Flocking and Locking -- 7.6 P-Binding Capacity -- 7.7 Calculating Dose Rates -- 7.8 Other Issues -- 7.9 Future Prospects -- 7.9.1 Sediment Capping Targeting N -- 7.10 Conclusions -- References -- Chapter 8: Control of Invasive Aquatic Plants -- 8.1 Introduction -- 8.1.1 Native Flora -- 8.1.2 Invasive Aquatic Plants and Their Impacts -- 8.1.3 Recognising a Weed -- 8.2 How Weeds Can Be Managed to Restore Biodiversity in Lakes -- 8.2.1 Control Tools -- 8.2.1.1 Habitat Manipulation -- 8.2.1.2 Mechanical and Manual Control -- 8.2.1.3 Biological Control -- 8.2.1.4 Chemical Control -- 8.2.1.5 Integrated Control -- 8.3 Management Targets: Restoring Function and Indigenous Values -- 8.3.1 Nuisance Control -- 8.3.2 Restoration -- 8.3.3 Eradication -- 8.3.4 Monitoring and Surveillance of Aquatic Weeds for Lake Restoration -- 8.4 Examples of Controlling Invasive Aquatic Weeds and Restoration Outcomes for Lakes. , 8.4.1 Management Strategies for Large Lakes or Regions -- 8.4.1.1 Lake Wanaka -- 8.4.1.2 Northland Region: Lakes Prioritisation, Surveillance, Incursion Response, and Eradication Progress -- 8.4.2 Selective Target Weed Control -- 8.4.2.1 Lake Okataina -- 8.4.2.2 Yellow Flag Iris in Lake Rotoroa -- 8.4.3 Eradication of Invasive Aquatic Plants to Enable Native Plant Regeneration -- 8.4.3.1 Endothall to Eradicate Hornwort and Lagarosiphon -- 8.4.3.2 Grass Carp to Eradicate Egeria and Hydrilla -- 8.5 Future Prospects -- 8.5.1 New Species Detections and `Sleeping Giants´ -- 8.5.2 Climate Change -- 8.5.3 The Tool Box -- References -- Chapter 9: Management of Non-indigenous Lacustrine Animals -- 9.1 Introduction -- 9.2 Inventories and Distributions -- 9.2.1 Invertebrates -- 9.2.2 Fish -- 9.2.3 Other Vertebrates -- 9.3 Review of Control Techniques -- 9.3.1 Pre-border Controls -- 9.3.2 Border Control -- 9.3.3 Post-border, Pre-establishment Management -- 9.3.4 Post-establishment Control Measures: Invertebrates -- 9.3.5 Control Measures: Vertebrates -- 9.4 Conclusions and Future Prospects -- References -- Chapter 10: Restoration of Native Fish in New Zealand Lakes and Reservoirs -- 10.1 Introduction -- 10.2 Littoral Habitat Restoration -- 10.2.1 Smelt -- 10.2.2 Dwarf Inanga -- 10.2.3 Common Bully -- 10.3 Restoring Connectivity -- 10.3.1 Longfin and Shortfin Eels -- 10.4 Piscivore Control -- 10.4.1 Perch Predation on Common Bully -- 10.4.2 Trout Predation on Galaxias in Dune Lakes -- 10.4.3 Trout Predation on Banded Kokopu -- 10.4.4 Trout Predation on Koaro -- 10.5 Translocation -- 10.5.1 Common Bully -- 10.5.2 Smelt -- 10.5.3 Dwarf Inanga -- 10.6 Future Prospects -- References -- Chapter 11: Indicators of Ecological Integrity -- 11.1 Ecological Integrity -- 11.1.1 New Zealand Definitions of Ecological Integrity. , 11.2 Key Attributes of Lake Ecological Integrity.