Lake Rerewhakaaitu in the Bay of Plenty Region of North Island, has one of the most intensively farmed lake catchments in New Zealand. Nitrate concentrations in two surface stream inflows to the lake show substantial and statistically significant increases, between 1995 and 2015, however, lake water quality has remained relatively stable. The lake is polymictic (i.e., it mixes frequently) and is partly perched, with an effective hydrological catchment of approximately 10% of the surface topographic catchment. We used the hydrodynamic-ecological model DYRESM-CAEDYM to examine the relationship between inflow quantity and quality, and lake water quality. A groundwater model (MODFLOW) provided groundwater discharge values from the hydrologically effective catchment, to the lake model (DYRESM-CAEDYM). The model successfully reproduced the magnitude and dynamics of field measurements, as evidenced by low statistical error. Based on a novel uncertainty analysis that allows for assessment of forcing factors that contribute to model error, a component of the statistical error was identified to be due to lake water level variations, which was attributed to ecological changes in the littoral (shallow-water) zone of the lake. The calibrated model was used with a set of scenarios to examine land use change within the effective hydrological catchment, as well as climate change. Establishment of the lake model was subject to several areas of substantial uncertainty, including derivation of stream inflows by statistical modelling (rather than direct observation), hydrological uncertainty with regard to drainage pathways in the lake catchment, and reliability of some nutrient measurements in the lake and streams. Nevertheless, the present model can be considered among the most sophisticated tools available with which to inform lake management decisions. Model results suggest that improved land management efforts within the wider topographic catchment will have only minor impacts on Lake Rerewhakaaitu water quality, but within the hydrologically effective catchment land use improvements to decrease losses of nitrogen and phosphorus to the lake will be important. Maintaining and/or enhancing the forested area within the hydrologically effective catchment and potentially retiring (to indigenous vegetation) some of the area, as well as maintaining the riparian buffer of the lake, will help to maintain water quality of Lake Rerewhakaaitu. The model predicted that a future warmer climate would likely increase the duration of temperature stratification in the water column, leading to more deoxygenation of bottom waters and a decline in water quality. Offsetting this with maintaining and enhancing vegetation in the riparian area and hydrologically effective catchment may help to offset these effects.