The Time Series Station Boknis Eck (BE), initiated in 1957, is one of the longest operated time series stations worldwide. We present the first statistical evaluation of a dataset of nine physical, chemical and biological parameters in the period of 1957–2013. In the past 3 to 5 decades, all of the measured parameters underwent significant long-term changes. Most striking is an ongoing decline in bottom water oxygen concentration, despite a significant decrease of nutrient and chlorophyll a concentrations. Temperature enhanced oxygen consumption in the bottom water and a prolongation of the stratification period are discussed as possible reasons for the ongoing oxygen decline despite declining eutrophication. Observations at the location BE were compared with model output of the Kiel Baltic Sea Ice Ocean Model (BSIOM). Reproduced trends were in good agreement with observed trends for temperature and oxygen, but generally the oxygen concentration at the bottom was overestimated.