Bacterioplankton abundance and production were followed during one decade (1991–2001) in the hypertrophic and steeply stratified small Lake Verevi (Estonia). The lake is generally dimictic. However, a partly meromictic status could be formed in specific meteorological conditions as occurred in springs of 2000 and 2001. The abundance of bacteria in Lake Verevi is highly variable (0.70 to 22 × 106 cells ml−1) and generally the highest in anoxic hypolimnetic water. In 2000–2001, the bacterial abundance in the hypolimnion increased probably due to meromixis. During a productive season, heterotrophic bacteria were able to consume about 10–40% of primary production in the epilimnion. Our study showed that bacterioplankton in the epilimnion was top-down controlled by predators, while in metalimnion bacteria were dependent on energy and carbon sources (bottom-up regulated). Below the thermocline hypolimnetic bacteria mineralized organic matter what led to the depletion of oxygen and created anoxic hypolimnion where rich mineral nutrient and sulphide concentrations coexisted with high bacterial numbers.