Decadal-scale variations of ecosystem productivity in the Bohai Sea are described by using the survey data of 1959–60, 1982–83, 1992–93 and 1998–99. Indices including chlorophyll a concentration, primary production, phytoplankton abundance, zooplankton biomass and fishery biomass were used to describe the ecosystem productivity at different trophic levels. During the past four decades, the productivity and community structure of the Bohai Sea ecosystem has been highly variable. Primary productivity and fish productivity decreased from 1959 to 1998, such that phytoplankton abundance in 1992 and 1998 was about 38% of that in 1959 and 1982, fishery biomass in 1998 was particularly low, which was only about 5% of that in 1959. Zooplankton secondary productivity also showed a decreasing trend from 1959 to 1992, but reached high levels in 1998, about three times as much as 1959 and 1982, and four times as much as 1992. These results indicate that a large variation in ecosystem productivity is one of the important characteristics of coastal ecosystem dynamics. Therefore, it is impossible to apply a single theory to explain the causes of variations in the Bohai Sea ecosystem as the changes in productivity are likely to be forced and/or modulated by multiple mechanisms.