Effects of suspended mussel and infaunal clam cultivation on sediment characteristics, and benthic organic and inorganic nitrogen and phosphorus fluxes were compared in a shallow coastal lagoon. The two species had different impacts on sediment features, but both created "hotspots" of nutrient fluxes with annual N and P regeneration rates being 4.9 and 13.5 (mussel) and 4.5 and 14.9 (clams) fold greater than those of unfarmed control sediments. Mussel farming also caused considerable nutrient regeneration within the water column with the mussel ropes contributing ~25% of total inorganic N and P production and at times dominating the sediments (e.g. 95% of SRP production in summer and 45% of DIN production in winter). Such nutrient regeneration rates seriously question the proposal that suspension-feeding bivalves act as a eutrophication buffer, especially during summer when nutrient regeneration rates are maximal, but other nutrient sources (freshwater run-off and unfarmed sediments) are at their lowest.