Dissolved C, N, P, and Si budgets for Tomales Bay, California, have been used to solve simultaneous stoichiometric equations which describe a plausible material balance for net organic matter reactions in the bay. Dissolved Si and P were both exported hydrographically. Dissolved C and fixed N were imported hydrographically. If we assume that C, N, P, and Si were supplied to the bay as organic detritus and remineralized at a rate required to balance dissolved Si and P exports, we can calculate reasonable rates of denitrification and CO2 gas evasion across the air-water interface. The system is thus interpreted to have been net heterotrophic at the time of our investigation.Fluxes attributed to individual components in the system (benthic respiration, water-column material turnover, biochemical transformations between fixed and gaseous N) were of sufficient magnitude to account for the system-wide net fluxes, although too noisy to allow piecewise derivation of net system fluxes. Denitrification and limitation of primary production by dissolved fixed N in aquatic ecosystems may be symptoms of other system-scale constraints on net C metabolism, rather than themselves being system-level controls of net C metabolism.