Cycling of methane (CH4) in Tomales Bay, a 28-km(2) temperate estuary in northern California with relatively low inputs of organic carbon, was studied over a 1-yr period. Water column CH4 concentrations showed spatial and temporal variability (range = 8-100 nM), and were supersaturated with respect to the atmosphere by a factor of 2-37. Rates of net water column CH4 production-oxidation were determined by in situ experiments, and were not found to be significantly different from zero. Fluxes across the sediment-water interface, determined by direct measurement using benthic chambers, varied from -0.1 mu mol m(-2) d(-1) to +16 mu mol m(-2) d(-1) (positive fluxes into water). Methane concentrations in the two perennial creeks feeding the bay varied annually (140-950 nM); these creeks were a significant CH4 source to the bay during winter. in addition, mass-balance calculations indicate a significant additional winter CH4 source, which is hypothesized to result from storm-related runoff from dairy farms adjacent to the bay. Systemwide CH4 budgets of the 16-km(2) inner hay indicate benthic production (110 mol d(-1)) and atmospheric (110 mol d(-1)) dominated during summer, while atmospheric evasion (160 mol d(-1)) and runoff from dairy farms (90 mol d(-1))dominated during winter.