We investigated habitat use and diversity of waterbirds at one of the coastal and satellite lagoons around Lake Biwa, which is a registered wetland of the Ramsar Convention in Japan. To evaluate the importance for waterbirds of a lagoon around the freshwater lake, we conducted 26 censuses over 1 year on seven blocks with different landscape elements in a small lagoon. A total of 25 species were found and most of them (72%) belonged to a guild in which birds forage without diving. Species density (per ha) and diversity was high in blocks where Zizania latifolia Turcz and Phragmites australis L. reed beds existed. Not all of the waterbird species were feeding all the time, but were often resting in their preferred blocks, suggesting that they use the lagoon as both a refuge and a feeding site. Habitats with a structural reed bed community and shallow waters (<1 m depth) may be crucial determinants of high waterbird diversity in this small lagoon around which many people live.