In several countries around the world, agricultural land area exceeds 70% (Uruguay 82.6%, Kazakhstan 80.4%, Turkmenistan 72.0%, Great Britain 71.7%, Ukraine 71.6% and others). This poses a serious risk of dissipating nitrates into the aquatic environment in agricultural catchments. The aim of this study was to assess the impact of land use on water quality parameters in an agricultural catchment area. It was decided to select for analysis the catchment of the Orla River (river length of 88 km, catchment area of 1,546 km2). The catchment area is predominantly agricultural in character and its entire area has been declared as an agricultural nitrate vulnerable zone (NVZ). A total of 27 survey sites were selected on the main watercourse and its tributaries. Analyses were conducted in the years 2010–2012 to determine physical and chemical parameters of water (pH reaction, conductivity, dissolved oxygen, total nitrogen, organic nitrogen, ammonia nitrogen, nitrates, total and reactive phosphorus) as well as six macrophyte metrics of ecological status assessment (MIR, IBMR, RMNI, MTR, TIM, RI). The average values of most physico-chemical parameters of water quality repeatedly exceeded limits of good ecological status, both in the Orla River and its tributaries. As many as 18 survey sites were classified as moderate ecological status, five sites as poor and only four as good ecological status. The results indicate the impact of land use in the catchment on water conductivity. Differences were observed in the concentrations of biotic components in the main watercourse and its tributaries, and in water quality in the southern part of the catchment in relation to the rest of the study area. This is probably connected with a greater share of forests and surface waters in that area.