The spatial and temporal dimensions of environmental impacts of climate and land cover changes are two significant factors altering hydrological processes. Studying the effects of these factors on water quality, provides important insight for water resource management and optimizing land planning given increasing water scarcity and water pollution. The impact of land cover and climate changes on surface water quality was assessed for the Neka River basin in Northern Iran. The widely used Soil and Water Assessment Tool (SWAT) was applied for pollutant modeling, and was calibrated using the Sequential Uncertainty Fitting (SUFI-2) algorithm. An ensemble of 17 CMIP5 climate models under two IPCC greenhouse gas emission scenarios were selected, and future land cover change (LCC) was modeled based on the evolution that occurred in the last decades. We simulated the impacts of climate change (CC) and LCC on sediment, nitrate, and phosphate for the 2035–2065 time slice. The annual loads of sediment, phosphate, and nitrate are projected to decrease under both CC scenarios based on the inter-model average, and generally follow a pattern similar to the change in river discharge. Nitrate concentrations show an increase across all seasons, while the sediment and phosphate concentrations increase in winter and autumn under CC conditions. Results indicate that pollutants are expected to increase under LCC alone, mainly due to the expansion of the cultivated areas. Overall, it seems CC has a greater impact than LCC on the variation of water quality variables in the Neka River basin. With a combined change in climate and land cover, the annual nitrate concentrations are expected to increase by + 19.7% and + 17.9%, under RCP 4.5 and RCP 8.5, respectively. The combined impacts of the CC and LCC caused a decline in the annual sediment and phosphate concentrations by −10.1% and −2.2% under RCP 4.5 and −9%, and −3.2% under RCP 8.5, respectively.

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