Büyük Menderes catchment, located in the southwestern part of Turkey, is one of the most populated river basins in Turkey with 2.5 millions inhabitants. Due to increasing activities in agriculture and industrial sectors, water resources management in the basin is one of the biggest matters for the future. During the past decade, it has been observed a basinwide shift to larger monocultural, intensively operated farm units. Therefore, there is land use conversion from native lands to agriculture. The threat of nutrients pollution, nitrogen and phosphorus, has become a preoccupation since many lands and rivers undergo a eutrophication process. The discharge of nutrients from Büyük Menderes basin to the Aegean Sea through Büyük Menderes river also needs to be reduced in order to bring the eutrophication problems under lasting control. In this paper, the PolFlow model embedded in PCraster is applied to the catchment for quantifying water and substances fluxes for the five-year period, 1999–2004. The implementation of the model in the catchment allows describing the water balance and thus nutrient transport on the landscape surface but also through the soil and aquifer's layers. Modeling process is complicated by the transfer of nutrients from diffuse and point-source emissions, managed by retention and periodic release from storages within the catchment. Modeling diffuse and point-source nutrient emissions contribution to river loads can be improved by better knowledge about spatial and temporal distribution of this retention and release in the basin.

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