Abstract To contribute to the validation of a recently developed ecosystem model of the western Wadden Sea (EON, 1988), data on bacterial biomass and production were acquired. Seven field stations, spread over the two main basins of the estuarine system, were sampled monthly in 1986. Between these basins significant differences were found in counts, biovolume, biomass and production of bacteria (measured by the 3H-thymidine method) with consistently higher mean values of bacterial variables in the Vlie basin. Bacterial production rates of 2 to 175 mg C· m−3· d−1 were obtained for the Vlie basin, with an annual production of 10 to 11 g C· m−3, while the production in the Marsdiep basin did not exceed 45 mg C·m−3 ·d−1, with an annual production of g C·m−3. Bacterial biomass varied over the year from 2 to 140 mg C·m−3 in the study area, with a mean biomass of 39 mg C·m−3 in the Vlie basin and 23 mg C·m−3 in the Marsdiep basin. Blooms of bacteria occurred in May and July–August. Spatial and temporal fluctuations in bacterial variables are discussed, taking into account different environmental factors and the availability of food for bacteria in relation to transport and exchange of water masses between the two basins and the North Sea. Results are compared with the results as simulated by the ecosystem model.