Nutrient concentrations and phytoplankton biomass were monitored with reference to several anthropogenic pressures in the Karamenderes River (Canakkale, NW Turkey) and in its catchment through a seasonal sampling program of three sites. Both spatial and temporal variations in chl a, nitrate and nitrite and temporal variation in ammonium, phosphate and silicate were significant. Despite intense application of chemical fertilizers in agricultural areas within the catchment and elevated riverine nitrate concentrations phosphate levels were low, potentially keeping chl. a levels in oligotrophic range. Considering the important role of phosphorus in freshwater eutrophication and complex dynamics of phosphorus leaching from soil, the healthy functioning of this ecosystem critically depends on management plans that consider the long term risks associated with phosphate transfer from agricultural soils into the river.