To quantify the effects of a future climate on three morphologically different lakes that varied in trophic status from oligo-mesotrophic to highly eutrophic, we applied the one-dimensional lake ecosystem model DYRESM-CAEDYM to oligo-mesotrophic Lake Okareka, eutrophic Lake Rotoehu, both in the temperate Bay of Plenty region, and highly eutrophic Lake Ellesmere, in the temperate Canterbury region, New Zealand. All three models were calibrated for a three-year period and validated for a separate two-year period. The model simulations generally showed good agreement with observed data for water column temperature, dissolved oxygen (DO), total phosphorus (TP), total nitrogen (TN) and chlorophyll a (Chl a) concentrations. To represent a possible future climate at the end of this century, mean annual changes in air temperature by 2100, derived from the IPCC A2 scenario downscaled for these lake regions, were added to the daily baseline temperatures for years 2002–2007. Lake model simulations using this future climate scenario indicate differential increases in eutrophication in all three lakes, especially during summer months. The predicted effects on annual mean surface water concentrations of TP, TN and Chl a will be equivalent to the effects of increasing external TN and TP loading by 25–50%. Simulations for the polymictic, eutrophic Lake Rotoehu further indicate that cyanophytes will be more abundant in the future climate, increasing by >15% in their contribution to annual mean Chl a. Therefore, future climate effects should be taken into account in the long-term planning and implementation of lake management as strategies may need to be refined and adapted to preserve or improve the present-day lake water quality.