Benthic fluxes of dissolved nutrients, oxygen, dissolved inorganic carbon, and total alkalinity were measured over a 2 yr period in Tomales Bay, California, USA, using in situ incubation chambers. Release of dissolved nutrients from the sediment peaked in late summer and was lowest in winter. The difference between C:N:P flux ratios and composition of suspended particulates indicated the existence of a sink for regenerated N, relative to C and P. Total alkalinity flux revealed that carbon metabolism by net sulfate reduction represented ca one-third of total benthic metabolism. Partitioning net system fluxes into component fluxes suggested that the equivalent of ca 70 to 80% of the available particulate C, N and P was respired within the water column, while about 20 to 30% was respired by the benthos. During spring, increasing light resulted in higher water column productivity, followed closely by rising water column respiration. With low delivery of the new organic material to the benthos, and low residual organics in the sediment, benthic respiration remained low. Fallout of particulate material, coinciding with peak water temperature in late summer, resulted in a 'crossover' with benthic respiration temporarily exceeding water column respiration.