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The impact of a sea bass (Dicentrarchus labrax L., 1758) farm on water quality and benthic community structure was investigated at a fish farm site in Engeceli Bay (western part of Izmir Bay) between April 2001 and February 2002. The characteristics of the water column in the fish farm were investigated in terms of physical and chemical parameters. Concentrations of nitrate, phosphate and ammonium ions in all sampling stations within the Bay were compared with the water quality parameters measured at the outer part of Izmir Bay (Eastern Aegean Sea). While there were significant differences from season to season of the levels of ammonium, orthophosphate, total phosphate and nitrite, there were no significant differences among stations. However, nitrate values and organic carbon contents showed significant differences among sampling stations. A reference station was selected to compare benthic groups. While the reference site is characterized by a sandy bottom with the lowest carbon and highest diversity values, the other stations with silty‐clay bottoms showed higher organic enrichment and lower diversity with increasing abundance of polychaeta. Organic enrichment and particle size of sediments were closely associated with faunal groups particularly with polychaeta and mollusca.

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