Water pollution with nutrients (nitrogen and phosphorus) is nowadays one of the main environmental issues in the Baltic Sea region. The use of fertilizers in agricultural lands is considered as one of the most common source of environmental pollution. This research examines water quality in the Mellupite catchment – a territory with moderate agricultural intensity. It has been determined that hydrological characteristics of the research territory is highly affected by factors such as scale, topography, subsurface drainage intensity and the share of agricultural land in the catchment. This research addresses agricultural land use issue – explores connections between agricultural land use and water quality. Our results suggest that the agricultural land use of the research territory is diverse, but two dominant crop types stands out – grasslands and winter wheat. In general, the summer crops are dominant in the Mellupite catchment, but the distribution of summer and winter crops has become more equal in time from 2005 to 2014 most likely because of increasing demand of rapeseed oil and meal. Connections between crop area and P amount have been observed. Strong correlation between grasslands and phosphorus loads in winter period have been observed, most likely caused by manure as organic fertilizer used late autumn. To confirm causes of crops’ area and nutrient load correlations additional research including detailed fertilizer use should be made.