ISSN 2463-6029 (Print) ISSN 2350-3432 (Online) Waikato Shallow Lakes Modelling 2017 ERI Report 94 Client report prepared for DairyNZ, Waikato River Authority, Waikato Regional Council, DOC/Fonterra Living Waters Partnership and Waipa District Council By Moritz K. Lehmann, David P. Hamilton, Kohji Muraoka, Grant W. Tempero, Kevin J Collier and Brendan J Hicks Environmental Research Institute University of Waikato, Private Bag 3105 Hamilton 3240, New Zealand Waikato Shallow Lakes Modelling Cite report as: Lehmann, M. K., Hamilton, D. P., Muraoka, K., Tempero, G. W., Collier, K. J., Hicks, B. J. 2017. Waikato Shallow Lakes Modelling. ERI Report 94. Environmental Research Institute, University of Waikato, Hamilton, New Zealand. 223 pp. Cover photo: Lake Ngāroto on a calm day in November 2015. Disclaimer: The information and opinions provided in this Report have been prepared for the Client and its specified purposes. Accordingly, any person other than the Client, who uses the information and opinions in this report, does so entirely at their own risk. The Report has been provided in good faith and on the basis that reasonable endeavours have been made to be accurate, not mislead in any way, and to exercise reasonable care, skill and judgment in providing information and opinions contained therein. Neither the University of Waikato, nor any of its employees, officers, contractors, agents or other persons acting in its behalf or under its control, accepts any responsibility or liability to third parties in respect of any information or opinions provided in the Report. Report reviewed by: Approved for release by: Marnie Campbell John Tyrrell University of Waikato University of Waikato 2 Waikato Shallow Lakes Modelling Executive Summary The principal aim of this study is to apply a modelling approach to identify, evaluate and prioritise specific in-lake and catchment restoration options which could be applied to improve the water quality and ecological health of peat and riverine lake types across the Waikato Region. Four representative lakes have been selected as case studies for this work based on their social, cultural and ecological significance, as well as the availability of historical monitoring data and the potential transferability of the study findings to similar lake systems. The lakes include Rotomānuka, Ngāroto, Waahi and Waikare. This study comprises the following six objectives for each lake: 1. Define baseline water quality and ecological health based on existing monitoring data and knowledge. 2. Determine the key pressures, drivers and processes governing lake water quality and ecological health. 3. Define, evaluate and rank the likely effectiveness of a range of in-lake and catchment management strategies to improve existing water quality and biodiversity values. 4. Evaluate the level of certainty around the suggested restoration strategies that meet the desired outcomes, as well as the timeframes implementation and longevity. 5. Identify an achievable end state for water quality and ecological health, taking into consideration existing trophic state, legacies and catchment land use. 6. Provide an expert assessment on whether the strategies identified are also likely to be effective when applied to other similar Waikato lake types. Process-based dynamic modelling was chosen for this study because it can be used to test the plausibility of conceptual models of lake ecosystem function, to shed light on the importance of various processes contributing to observed system behaviour, and to extrapolate to future scenarios that fall outside the range of historical observations. This report consists of a main body of text with an Extended Conclusions section that goes into detail about processes in the lakes that are relevant to understanding management, as well as 7 appendices. For modelling of one-dimensional (1-D) lake hydrodynamics and ecological processes, we chose the one-dimensional, coupled hydrodynamic-ecological model DYRESM-CAEDYM as the tool for 3 Waikato Shallow Lakes Modelling assessing effects of altered hydrology, nutrient and sediment loads, and climate on physical and biogeochemical processes in Lakes Ngāroto, Waahi and Rotomānuka. Modelling of three- dimensional (3-D) hydrodynamics of Lake Waikare was initiated using Delft3D-FLOW but not progressed to the point of presenting simulations given the time constraints of the present study. Catchment boundary conditions consisting of time series of discharges and contaminant loads for each of the lakes were generated using either the process-based INtegrated CAtchments model (INCA), the TopNet hydrological model or mass-balance calculations from known water level and outflow data, with measured data used to check the veracity of assumptions and model outputs. Multiple lake management scenarios were conceptualised with a project working group and these were simulated using a DYRESM-CAEDYM model calibrated to each lake application (Ngāroto, Waahi and Rotomānuka). The management approaches assessed can be broadly considered as belonging to three categories: 1. External nutrient load reduction: associated with land use change or other nutrient loss reductions from improved management practices and/or targeted interventions, e.g., erosion control, denitrification beds; 2. Hydrological modifications: diversion of inflows away from the lake or increasing the water level to alter wind-driven resuspension of sediments; 3. Geochemical engineering: by using sediment capping to reduce internal loading and/or continuous low-dosage alum treatment to reduce dissolved P and increase flocculation in the water column. The base model and each scenario simulation are presented and compared using metrics which describe the water quality in terms of summary statistics, for example, attribute bands (A, B, C or D) from the National Objectives Framework (NOF) of the National Policy Statement for Freshwater Management (NPS-FM, MfE 2015a). Lake Ngāroto Lake Ngāroto is the largest of the Waipa peat lakes (surface area of 108 ha) and is important for its cultural history and for recreational activities. Its current mean depth is c. 2 m and maximum depth 4 m. The Lake Ngāroto catchment is predominantly dairy pasture, resulting in high external nutrient loads to the lake. The high nutrient load, shallow depth, loss of submerged macrophytes and reduced lake volume (compared with historical levels) have collectively led to resuspension of bottom sediments, high water column turbidity and high levels of internal nutrient loading. Lake Ngāroto has recurrent algal blooms, hosts large populations of invasive fish including catfish, rudd, 4 Waikato Shallow Lakes Modelling gambusia, goldfish and koi carp, but also has valuable native fish populations including common bullies, shortfin eels and common smelt. Isotope data from this study indicate that the food base is dominated by organic matter, most likely primarily of terrestrial origin but with some seasonal variability, and large eels are at the top of the food web but with potential for some overlap of diet with catfish and koi carp. The lake model for Ngāroto showed an acceptable match to observations of temperature, surface and bottom dissolved oxygen (DO), total nitrogen (TN), total phosphorus (TP), total suspended solids (TSS) and chlorophyll a, though observed data were quite sparse for deriving input data to the lake model and for comparisons with model outputs. In-lake data were repeated over a five-year period from one year of measured data for the purpose of model comparisons. There was also limited data on inflow composition to derive a daily inflow file consisting of discharges and concentrations of TSS and nutrient species. The model was most sensitive to parameters relating to the density of particulate organic matter, reinforcing that it would be useful to quantify the size and nature of suspended material in the water column of Lake Ngāroto, as well as establishing setting velocities. Parameters affecting the dynamics of cyanobacteria and temperature responses were also particularly sensitive. Fourteen simulations were carried out for Lake Ngāroto to examine water quality effects of changes in external (catchment) loads, internal (bottom-sediment) loads, water level changes and an inflow (Ngārotoiti) diversion. Despite reductions in internal and external nutrient loads of up to 50%, no scenario resulted in NOF status of the lake improving from the D band. The scenario most effective at reducing median total phosphorus (TP), total nitrogen (TN) and chlorophyll a (TCHLA) was N14 (50% external reduction for P and 50% anoxic release reduction for P). This simulation might equate to some land use change and improved land management practices, as well as geochemical engineering to reduce the internal (bottom-sediment) nutrient load. Comparisons between scenarios which combine internal and external load reductions in N and P in various combinations (e.g., N3, N7, N13 and N14) suggest that chlorophyll a concentration is driven reasonably evenly by external and internal nutrient loading, with much of the internal loading occurring during summer when phytoplankton growing conditions are most suitable (i.e., warmer water temperature and higher irradiance). For Lake Ngāroto to meet the bottom line in the NOF within the next 3-4 decades will require intensive catchment actions that will ultimately reduce the level of nutrient enrichment in the bottom sediments. Perhaps more importantly, however, and with a much higher risk in terms of