[en] Highlights: • Habitats in three Baltic Sea Chemical Warfare dumpsites were described as Deep-Sea Muddy Sands. • All investigated basins belong to so-called “benthic-deserts”. • Multidisciplinary studies have been performed. • Dumpsites were investigated before, during and after a Major Baltic Inflow event. • Temporary Return of benthic macrofauna was observed in one basin. The Baltic Sea is a severely disturbed marine ecosystem that has previously been used as a dumping ground for Chemical Warfare Agents (CW). The presence of unexploded underwater ordnance is an additional risk factor for offshore activities and an environmental risk for the natural resources of the sea. In this paper, the focus is on descriptions of the marine habitat based on the observations arising from studies linked to the CHEMSEA, MODUM and DAIMON projects. Investigated areas of Bornholm, Gotland and Gdańsk Deeps are similarly affected by the Baltic Sea eutrophication, however, at depths greater than 70 m several differences in local hydrological regimes and pore-water heavy metal concentrations between those basins were observed. During the lifespan of presented studies, we were able to observe the effects of Major Baltic Inflow, that started in December 2014, on local biota and their habitats, especially in the Bornholm Deep area. Reappearance of several meiofauna taxa and one macrofauna specimen was observed approximately one year after this phenomenon, however it's ecological effects already disappeared in March 2017. According to our findings and to the EUNIS Habitat Classification, the three reviewed areas should be characterized as Deep Sea Muddy Sands, while the presence of suspicious bomb-like objects both beneath and on top of the sediments confirms their CW dumpsite status.