Shallow lakes in the semi-arid climate zone of the Mediterranean are sensitive to drought due to the low annual precipitation and high evaporation. Changes in precipitation and temperature as projected by climate change scenarios will have an effect on the hydrology of these shallow lakes with secondary effects on nutrient dynamics and ecological state. In this study, we used a combined modelling approach that included the catchment model Soil and Water Assessment Tool (SWAT) and the lake model PCLake to study the possible effects of several climate scenarios on a shallow lake in semi-arid central Anatolia, Turkey. Our results show that lower precipitation and higher temperatures may reduce inflow rates and water levels drastically. Diffuse nutrient loading depended highly on precipitation and thus decreased as well. The lake model predicts an interaction between external nutrient loading and water levels. Low water levels benefited submerged macrophytes if nutrient concentrations were low, but low inflow rates and high evaporation during dry periods increased in-lake nutrient concentrations and chlorophyll-a. Cyanobacteria biomass was also higher in the drier and warmer scenarios. Overall, the results show that lower hydraulic loads and reduced flushing rates as a result of drier and warmer conditions lead to lower water levels and higher in-lake nutrient concentrations unless nutrient loading decreased as well. This implies that catchment-scale nutrient management is essential to maintain low nutrient concentrations in the lakes with increasing temperature and decreasing precipitation in a dry climate.