Trawling programmes in the Tyne estuary in North-east England have been conducted since 1982 by the Environment Agency, its predecessors and since 1990 by the Dove Marine Laboratory. Survey data have been combined and analysed to examine whether variations in the fish community can provide bio-indicators for changes in water quality following the installation of primary treatment works at Howdon. Changes in fish abundance and diversity after 1988 suggest a general decline in water quality in the lower estuary, which may be attributable to increases in the discharge from the treatment works. In contrast in the upper estuary changes in fish populations are commensurate with an improvement in water quality when outfalls were diverted to Howdon. Periods of change correspond with times of extension to the sewerage system. The Tyne fish community and the flounder population appear to provide reliable indicators of alterations in water quality.