Abstract. The SWAT model was modified to simulate the hydrologic and chemical response of karstic systems and assess the impacts of land use management and climate change of an intensively managed Mediterranean watershed in Crete, Greece. A methodology was developed for the determination of the extended karst area contributing to the spring flow as well as the degree of dilution of nitrates due to permanent karst water volume. The modified SWAT model has been able to capture the temporal variability of both karst flow and surface runoff using high frequency monitoring data collected since 2004 in addition to long term flow time series collected since 1973. The overall hydrologic budget of the karst was estimated and its evaporative losses were calculated to be 28% suggesting a very high rate of karst infiltration. Nitrate chemistry of the karst was simulated by calibrating a dilution factor allowing for the estimation of the total karstic groundwater volume to approximately 500 million m³ of reserve water. The nitrate simulation results suggested a significant impact of livestock grazing on the karstic groundwater and on surface water quality. Finally, simulation results for a set of climate change scenarios suggested a 17% decrease in precipitation, 8% decrease in ET and 22% decrease in flow in 2030–2050 compared to 2010–2020. A validated tool for integrated water management of karst areas has been developed, providing policy makers an instrument for water management that could tackle the increasing water scarcity in the island.