Description: Phytoplankton and bacteria are sensitive indicators of environmental change. The temporal development of these key organisms was monitored from 1988 to the end of 2007 at the time series station Boknis Eck in the western Baltic Sea. This period was characterized by the adaption of the Baltic Sea ecosystem to changes in the environmental conditions caused by the conversion of the political system in the southern and eastern border states, accompanied by the general effects of global climate change. Measured variables were chlorophyll, primary production, bacteria number, -biomass and -production, glucose turnover rate, macro-nutrients, pH, temperature and salinity. Negative trends with time were recorded for chlorophyll, bacteria number, bacterial biomass and bacterial production, nitrate, ammonia, phosphate, silicate, oxygen and salinity while temperature, pH, and the ratio between bacteria numbers and chlorophyll increased. Strongest reductions with time occurred for the annual maximum values, e.g. for chlorophyll during the spring bloom or for nitrate during winter, while the annual minimum values remained more stable. In deep water above sediment the negative trends of oxygen, nitrate, phosphate and bacterial variables as well as the positive trend of temperature were similar to those in the surface while the trends of salinity, ammonia and silicate were opposite to those in the surface. Decreasing oxygen, even in the surface layer, was of particular interest because it suggested enhanced recycling of nutrients from the deep hypoxic zones to the surface by vertical mixing. The long-term seasonal patterns of all variables correlated positively with temperature, except chlorophyll and salinity. Salinity correlated negatively with all bacterial variables (as well as precipitation) and positively with chlorophyll. Surprisingly, bacterial variables did not correlate with chlorophyll, which may be inherent with the time lag between the peaks of phytoplankton and bacteria during spring. Compared to the 20-yr averages of the environmental and microbial variables, the strongest negative deviations of corresponding annual averages were measured about ten years after political change for nitrate and bacterial secondary production (~ −60%), followed by chlorophyll (−50%) and bacterial biomass (−40%). Considering the circulation of surface currents in the Baltic Sea we interpret the observed patterns of the microbial variables at the Boknis Eck time series station as a consequence of the improved management of water resources after 1989 and – to a minor extent – the trends of the climate variables salinity and temperature.