Using recent indices developed, in part, for use under the European Water Framework Directive (AMBI, BENTIX, BOPA, BQI, I2EC and the trophic index ITI), the ecological quality status of two highly contaminated environments--the Bay of Seine and the Seine estuary (Eastern English Channel)--was determined on several spatial and temporal scales. Data from 604 observations gathered over a 14-year period (1988-2002) were analyzed, and the results used to show the relationship between biotic indices, environmental variables and classic descriptors (e.g., number of species, total abundance, dominance index, ES(50) and Shannon/Brillouin diversities). Though the specific ecological quality (EcoQ) values calculated with the various indices were different, the overall trend of the results was similar. Synthesizing the values produced by the six indices used in the study allowed attribution of a high to good EcoQ status to the Bay of Seine and a moderate EcoQ to the estuary. The mesh size used when processing samples was proved to have no effect in winter on the EcoQ values for either body of water.