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.