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The poor water condition in agricultural watersheds in Poland provides evidence of a major impact of this sector on water quality, especially with regard to nutrients. What is specific about Polish agriculture, especially in the Wielkopolska region, is a large area of arable land and a high concentration of point sources. The outflow from these sources is very changeable and depends strongly on weather conditions, in particular precipitation. Therefore, it is very difficult to measure the runoff from those sources. This study presents a possibility of forecasting the pollution by main nutrients based on the land cover within the watersheds. It offers an option of using landscape metrics to identify the areas designed to protect waters against nitrate pollution by agriculture, or to locate the sampling sites. As many as 59 water quality indices were analysed for 259 measurement sites located on the rivers in the Warta basin (Poland). Next, an analysis of the land cover structure was performed for the watersheds located upstream of the measurement sites. As many as 14 landscape indices – measuring the composition and configuration in each watershed – were calculated using Fragstats 3.3. The results show clearly that the structure of the land cover within the watershed has a strong impact on water quality in lowland watersheds. Percentage of the arable land and land cover diversity indices, such as SHDI and Division, proved to be the best indicators of the amount of nutrients in water.