Measurements of benthic fluxes have been made on four occasions between February 1980 and February 198 1 at a channel station and a shoal station in South San Francisco Bay, using in situ flux chambers. On each occasion replicate measurements of easily measured substances such as radon, oxygen, ammonia, and silica showed a variability (& la) of 30% or more over distances of a few meters to tens of meters, presumably due to spatial heterogeneity in the benthic community. Fluxes of radon were greater at the shoal station than at the channel station because of greater macrofaunal irrigation at the former, but showed little seasonal variability at either station. At both stations fluxes of oxygen, carbon dioxide, ammonia, and silica were largest following the spring bloom. Fluxes measured during different seasons ranged over factors of 2-3,3,4-5, and 3-10 (respectively), due to variations in phytoplankton productivity and temperature. Fluxes of oxygen and carbon dioxide were greater at the shoal station than at the channel station because the net phytoplankton productivity is greater there and the organic matter produced must be rapidly incorporated in the sediment column. Fluxes of silica were greater at the shoal station, probably because of the greater irrigation rates there. N + N (nitrate + nitrite) fluxes were variable in magnitude and in sign. Phosphate fluxes were too small to measure accurately. Alkalinity fluxes were similar at the two stations and are attributed primarily to carbonate dissolution at the shoal station and to sulfate reduction at the channel station. The estimated average fluxes into South Bay, based on results from these two stations over the course of a year, are (in mmol mm2 d I): 02 = -27 + 6; TC02 = 23 f 6; Alkalinity = 9 f 2; N + N = -0.3 * 0.5; NH3 = 1.4 f 0.2; PO4 = 0. I f 0.4; Si = 5.6 f I. 1. These fluxes are comparable in magnitude to those in other temperate estuaries with similar productivity, although the seasonal variability is smaller, probably because the annual temperature range in San Francisco Bay is smaller.Budgets constructed for South San Francisco Bay show that large fractions of the net annual productivity of carbon (about 90%) and silica (about 65%) are recycled by the benthos. Substantial rates of simultaneous nitrification and denitrification must occur in shoal areas, apparently resulting in conversion to N2 of 55% of the particulate nitrogen reaching the sediments. In shoal areas, benthic fluxes can replace the water column standing stocks of ammonia in 2-6 days and silica in 17-34 days, indicating the importance of benthic fluxes in the maintenance of productivity.Pore water profiles of nutrients and Rn-222 show that macrofaunal irrigation is extremely important in transport of silica, ammonia, and alkalinity. Calculations of benthic fluxes from these profiles are less accurate, but yield results consistent with chamber measurements and indicate that most of the NH3, Si02, and alkalinity fluxes are sustained by reactions occurring throughout the upper 20-40 cm ...

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Nearly two decades of seasonal dissolved inorganic nutrient-salinity distributions in northern San Francisco Bay estuary illustrate interannual variations in effects of river flow (a nutrient source) and phytoplankton productivity (a nutrient sink). During winter, nutrient sources dominate the nutrient-salinity distribution patterns (nutrients are at or exceed conservative mixing concentrations). During summer, however, the sources and sinks are in close competition. In summers of wet years, the effects of increased river flow often dominate the nutrient distributions (nutrients are at or less than conservative mixing concentrations), whereas in summers of dry years, phytoplankton productivity dominates (the very dry years 197661977 were an exception for reasons not yet clearly known). Such source/sink effects also vary with chemical species. During summer the control of phytoplankton on nutrient distributions is apparently strongest for ammonium, less so for nitrate and silica, and is the least for phosphate. Furthermore, the strength of the silica sink (diatom productivity) is at a maximum at intermediate river flows. This relation, which is in agreement with other studies based on phytoplankton abundance and enumeration, is significant to the extent that diatoms are an important food source for herbivores.The balance or lack of balance between nutrient sources and sinks varies from one estuary to anotherjust as it can from one year to another within the same estuary. At one extreme, in some estuaries river flow dominates the estuarine dissolved inorganic nutrient distributions throughout most of the year. At the other extreme, phytoplankton productivity dominates. In northern San Francisco Bay, for example, the phytoplankton nutrient sink is not as strong as in less turbid estuaries. In this estuary, however, river effects, which produce or are associated with near-conservative nutrient distributions, are strong even at flows less than mean-annual flow. Thus, northern San Francisco Bay appears to be an estuary in between the two extremes and is shifted closer to one extreme or the other depending on interannual variations in river flow. Hydrobiologia 129, 37-58 (1985). 0 Dr W. Junk Publishers, Dordrecht. Printed in the Netherlands.

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