The University of Waikato was contracted by Waikato Regional Council to develop hydrodynamic models for Lake Whangape and Lake Waahi. The models are intended to provide a basis for future water quality modelling to inform the restoration of habitat for native fish and the management of pest fish populations. Lakes Whangape and Waahi are shallow, highly eutrophic lakes in the lower Waikato River basin. They contain significant populations of native fish species, such as īnanga (Galaxias maculatus), longfinned and shortfinned eel (Anguilla dieffenbachia and Anguilla australis). They also contain a number of exotic pest fish, such as mosquito fish (Gambusia affinis), koi carp (Cyprinus carpio) and goldfish (Carassius auratus), that can contribute significantly to water quality problems. For both lakes, bathymetry was combined with LiDAR (Light Detection and Ranging) data to create a topographic- bathymetric Digital Elevation Map (EDM) that provided the basis for the hydrodynamic model grids and may also be used for GIS modelling of potential fish habitat. The DEMs revealed the presence of stopbanks around both lakes that appear to restrict floodplain habitat significantly. Hydrodynamic models for Lakes Whangape and Waahi were developed using available measured or synthesised data. While there was insufficient data available for formal model calibration and validation, year-long model simulations were analysed to ensure that seasonal variability in water levels and temperature were represented. The model used, Delft3D-FLOW, is open-source, developed by Deltares (The Netherlands), and can be coupled to open-source ecological and water quality models (e.g. Delft-WAQ), thus enabling future water quality modelling applications.