Phosphorus is an essential nutrient which, however, leads to eutrophication when it is highly available in waters. The group of organic phosphorus compounds also plays an important role in this process, since some of them are also bioavailable. Two representatives of this group, about whose concentrations in aquatic systems only little is known, are the inositol phosphates and the natural phosphonates. This study investigates whether representatives of these two substance groups are present in aquatic systems on the German Baltic coastal area and how high their proportion of total organic phosphorus is. Selected substances for both groups were considered. Due to a lack of quantitative analytical methods, appropriate methods based on chromatography coupled with mass spectrometry were developed or adapted for all substances in a first step. In the next step these methods were used to detect the compounds inositol hexakisphosphate and methylphosphonic acid in samples from the aquatic systems mentioned above.