The Golden Gate National Recreation Area and the Point Reyes National Seashore include the surface waters of Tomales Bay, a twelve-mile long estuary that floods the northwest end of the fault-generated Olema Valley. The bay differs from other, generally shallower, Pacific coast estuaries and lagoons in having a much greater area of open water at low tide and therefore more waterbird habitat through the tidal cycle. Tide flats providing suitable habitat for most shorebird species are concentrated at opposite ends of the bay, in the vicinities of the deltas of Lagunitas and Walker creeks. In this report, we present an inventory of waterbirds and shorebirds in Tomales Bay during the winter of 1998-1999. The inventory is part of a larger effort to document avian distributions, relative abundances, species richness, and diversity in all major habitats of the three National Parks in the San Francisco Bay area: Point Reyes National Seashore, Golden Gate National Recreation Area, and the Presidio. Results of the waterbird and shorebird inventories are based on four baywide counts of waterbirds, conducted from boats, and seven baywide counts of shorebirds, conducted from shore. Abundances of gulls are excluded from the inventory because of difficulties in counting large numbers of transient birds and in identifying individuals to species.