The field data set obtained in 2015–2016 in the south-eastern part of the Baltic Sea within the exclusive economic zone (EEZ) of the Russian Federation revealed a rise in the values of the hydrological characteristics of the Gdansk and Gotland (southern slope) Basins bottom layer. It was caused by the increased frequency of the North Sea water intrusions and their advection into the bottom layer of basins. As a result of these intrusions the hydrochemical conditions of the near-bottom waters has changed. The highest values of the dissolved oxygen content coincided with the extremes of salinity and temperature. The content of phosphates and silica increased simultaneously with the decrease of concentration of dissolved oxygen. The variability of the parameters for two basins was different. An increase in the temperature and salinity values on the southern slope of the Gotland Basin was less obvious than that in the Gdansk Basin. The concentrations of dissolved oxygen within the Gotland Basin in the most cases (besides the spring 2016) exceeded the values in the Gdansk Basin by 0.3–1.0 ml/l. The oxidation of the bottom sediment upper layer was observed in the Gotland Basin's southern slope, while the Gdansk Deep sediments had distinct hydrogen sulfide smell. The benthic communities of the Gotland were represented not only by the species which are tolerant to low dissolved oxygen content, but also by the young Macoma balthica. Anaerobic periods led to the absence of benthic macro- and meiofauna in the deep areas of the Gdansk Basin.