We present munition compound data from the analysis of water column samples collected from the entire length of the German waters of Baltic Sea in March 2023 during ALKOR cruise AL590. Water column samples were collected from 93 sampling stations along a transect stretching from Flensburg Fjord to Usedom. Surface and deep-water samples were collected using a rosette of Niskin bottles. A CTD profile was also attached to the Niskin rosette frame. Samples (1L) were extracted onboard onto solid phase extraction (SPE) columns. Munition compounds were eluted from the SPE columns using acetonitrile, concentrated and reconstituted in 50% methanol/water. The samples were analyzed by ultra high-performance liquid chromatography and high-resolution, atmospheric pressure chemical ionization mass spectrometry.