Cruise POS530 (R/V Poseidon) sampled the water column throughout German territorial waters of the southwest Baltic Sea during 01-21 October 2018. The current dataset contains concentrations of dissolved munition compounds from Niskin bottle rosette casts between sea surface and seafloor. Vertical sampling resolution varied among stations, with a maximum of 9 sampling depths. Dissolved explosives in the samples were measured following Gledhill et al. (2019). Briefly, discrete samples (1 L) were preconcentrated onboard using solid-phase extraction. Target compounds were eluted with acetonitrile, further concentrated by evaporation, and measured by ultra-high performance liquid chromatography and high resolution heated electrospray ionization mass spectrometry.