Selenium (Se) variations in the water column, suspended particulate matter, and sediment through the salinity gradient, together with water-quality parameters, were investigated over four different river conditions: lowest–highest runoff and high–low production period between November 2004 and August 2005 in the plume of the Gediz River, Aegean Sea, Turkey. The drainage basin of the Gediz delta is predominantly agricultural and industrial in character. Dissolved Se exceeded the water-quality standard of 5 μg L–1 during high flow and varied from 9.4 μg L–1 to 0.02 μg L–1 through the salinity gradient during the study period. Particulate Se ranged from 5.2 μg L–1 to 0.02 μg L–1. Sediment in the river mouth was highly affected by Se contamination and reached a level greater than four times (7.6 μg L–1 dry wt) the background level. The results indicated that Se supplied by the river was removed rapidly from the water column before the salinity reached an average value of about 20 and accumulated within the delta.