The zooplankton of the northern San Francisco Bay estuary has been characterized over the last 2 decades by long-term declines in abundance of some species, and introductions of others. The most striking change occurred in 1987-88, concurrent with the spread of the introduced clam Potamocorbula amurensis. Previous work presented evidence suggesting that declines in some copepod species were caused by the clam, more by predation on nauplii than by competition for food. Here we show that the clam probably caused a decline in other species of zooplankton, and that the large decline in Neomysis mercedis was probably due to competition with P. amurensis for food. At the time of these declines in zooplankton the copepod Pseudodiaptomus forbesi became abundant over much of the region formerly occupied by the previously common copepod Eurytemora affinis. Based on present data, we cannot explain this apparent coincidence in timing, but assume it was due to a competitive interaction.

Although much of the post-clam period was characterized by drought, the low freshwater flows of that period do not explain the reduction in chlorophyll or zooplankton abundance. The high flows of 1993 caused a temporary reduction in abundance of P. amurensis, but the larger size of the clams made up for the reduction in numbers, and by summer the zooplankton populations were again low. The change in zooplankton distribution and abundance may persist into the future; however, it is not clear that higher trophic levels are being adversely affected.