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Reduction of nitrogen and phosphorus inputs into surface waters from nonpoint agricultural sources requires targeted application of differentiated measures. In the study focused on soil and water conservation in the Jihlava river basin upstream of the Dalešice reservoir, we identified areas at potential risk of soil erosion, elevated infiltration and nutrient leaching, tile-drained areas and vulnerable riparian zones of water bodies. We then designed a system of complex protective measures for this river basin in more variants, and their effectiveness was estimated using simple empirical model calculations and research findings. Application of the measures defined by optimal variant 3 in the studied watershed could lead to reduction of the soil erosion effects on the surface water quality by 26.5%, with simultaneous reduction of the amount of washed out total nitrogen by 22.8%. The results of our study constitute a partial component of the Qualitative Model of the Jihlava River Basin and they were provided for use to the Vysočina Region authorities and the State Land Office. [ABSTRACT FROM AUTHOR]