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Fast growing ephemeral algae are increasingly observed in shallow coastal waters worldwide. This is generally considered a symptom of coastal eutrophication. It has been suggested that the reoccurrence of macroalgal mats, despite ongoing efforts to decrease nutrient loadings, may be explained by the fact that sheltered bays function as self-regenerating systems through benthic regeneration of nutrients. The importance of benthic nutrient regeneration during the initiation of the growth of filamentous green algal mats was investigated in 2 shallow-water bays on the west coast of Sweden. Nutrient regeneration was assessed in situ and in the laboratory, using sediment-water light/dark incubations and pore water distribution patterns. Benthic efflux of inorganic nutrients could supply up to 55 to 100% of the estimated nitrogen demand and 30 to 70% of the phosphorus requirements for the initial macroalgal growth from May to June. However, the availability of the pore water nutrient pool was influenced by the amount and functional type of infauna, and by competition from microphytobenthos. Because of the internal nutrient source of the embayments, it is suggested that there may be a significant time lag between a decreased nutrient supply to coastal waters and improved conditions of shallow water embayments.