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Background Best management practices (BMPs) are promising solutions that can partially control pollution discharged from farmlands. These strategies, like fertilizer reduction and using filter strips, mainly control nutrient (N and P) pollution loads in basins. However, they have secondary impacts on nutrition production and ecosystem. This study develops a method to evaluate the cumulative environmental impacts of BMPs. It also introduces and calculates food’s environmental footprint (FEF) for accounting the total environmental damages per nutrition production. Methods This study combines the soil and water assessment tool (SWAT) for basin simulation with the indices of ReCiPe, a life cycle impact assessment (LCIA) method. By these means, the effectiveness of BMPs on pollution loads, production yields, and water footprints (WFs) are evaluated and converted as equivalent environmental damages. This method was verified in Zrebar Lake, western Iran. Here, water consumption, as WFs, and eutrophication are the main indices that are converted into equivalent health and ecological impairments. Two methods, entropy and environmental performance index (EPI), are used for weighting normalized endpoints in last step. Results Results showed that using 25–50% less fertilizer and water for irrigation combined with vegetated filter strips reduce N and P pollution about 34–60% and 8–21%, respectively. These can decrease ecosystem damages by 5–9% and health risks by 7–14%. Here, freshwater eutrophication is a more critical damage in ecosystem. However, using less fertilizer adversely reduces total nutrition production by 1.7–3.7%. It means that BMPs can decline total ecological damages and health risks, which threatens nutrition production. FEF presents a tool to solve this dilemma about the sustainability of BMPs. In the study area, a 4–9% decrease in FEF means that BMPs are more environmental friendly than nutrition menacing. Finally, this study concludes that SWAT-ReCiPe with FEF provides a quantitative framework for environment-food nexus assessment. However, due to the uncertainties, this method is recommended as a tool for comparing management strategies instead of reporting certain values.