The chemical and biological effects of biodeposition from a mussel culture were evaluated at multiple spatial scales during the summer of 2003 in Great-Entry Lagoon, eastern Canada. Sediment samples were collected directly under and between mussel lines (positions 10 m apart: 10 m scale) from multiple sites (located ca. 100 m apart: 100 m scale) in each of 3 zones: reference (R), 0+ and 1+ mussel cohort zones (located at least 500 m apart: km scale). In general, redox potential decreased and sulphide concentration increased with sediment depth but did not differ among zones or positions. A clear difference in macrofaunal community structure was observed among R, 0+ and 1+ zones, as well as between the positions directly under mussel lines in 1+ sites (1+(under)) and those between 1+ mussel lines (1+(between)). The benthic community at 1+(under) positions was dominated by an opportunistic species (Capitella capitata) and had the lowest diversity and biomass. 0+ sites were characterised by the greatest number of species and biomass, suggesting that some species have benefited from a moderate organic loading from the 0+ mussels. Historical data indicate that the deeper part of the lagoon was a naturally enriched environment. The mussel farm probably contributes to local organic enrichment. Comparison of benthic communities from the present study (>20 yr after the initiation of mussel aquaculture) in the site to similar historical data from 3 periods (1975 and 1978, before mussel farming; 1982, at the start of farming activities; and 2004, after the 1+ mussel harvest) showed that community structure differed largely because of the greater abundance of deposit feeders in 2003. However, among these 3 periods the differences in benthic community structure were no greater than differences observed between years within the periods.