Effective management of eutrophication in large, shallow, lakes is particularly challenging, especially in catchments dominated by agricultural activities. These challenges are further exacerbated in lakes that have undergone significant hydrological and biogeochemical modification. In these systems, effective hydrological management strategies may involve increasing discharge rates to promote flushing and modifying lake depth to reduce the effects of wind-induced sediment resuspension, while effective biogeochemical modification may involve improving catchment management practices to reduce external nutrient loading. In this study, we present a modelling investigation of Lake Waikare, Waikato, New Zealand; a large (surface area: 34 km²), shallow (mean depth: 1.2 m), hypereutrophic lake that has experienced significant hydrological modification and water quality deterioration since the early 1900s.