Water column samples were collected from 62 sampling stations along a transect stretching from Flensburg Fjord to the Bay of Mecklenburg in October 2022 during ALKOR cruise AL583. Here, we present metadata and munition compound data for the samples. Surface, mid-depth and deep-water samples were collected using a rosette of Niskin bottles. A CTD sensor package was also mounted on 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.