There is increasing evidence of environmental change impacts on freshwater ecosystem services especially through land use and climate change. However, little is known about how land conservation could help mitigate adverse water-sustainability impacts. In this paper, we utilized the InVEST tool and the Residual Trends method to assess the joint effects and relative contributions of climate change and land conservation on freshwater ecosystem services in the Portneuf River catchment in Idaho, USA. We developed five hypothesized scenarios regarding gain and loss in the enrollment of Conservation Reserve Program (CRP), the largest agricultural land-retirement program in the U.S., plus riparian buffer and assessed their interactions with climate change. Results suggest that the realized water yield in the Portneuf River catchment would possibly be 56% less due to climate change and 24% less due to the decline of CRP enrollment. On the contrary, if CRP enrollment is promoted by ~30% and riparian buffer protection is implemented, the water supply reduction in the year 2050 could be changed from 56% to 26%, the total phosphorus (TP) and total nitrogen (TN) export would be reduced by 10% and 11%, and the total suspended sediment (TSS) reduced by 17%. This study suggests that increasing implementation of the CRP would likely preserve key freshwater ecosystem services and assist proactive mitigation, especially for semiarid regions vulnerable to changing climate conditions.