In the young moraine landscape in Northeast Germany, small glacially created ponds, the so-called kettle holes, are very abundant. They exhibit large spatial heterogeneity, seemingly rendering each kettle hole unique. However, this would not be consistent with any scientific approach. Thus, a classification scheme has been developed for kettle holes in Northeast Germany based on morphology, hydrodynamics and connection to stream networks of the kettle holes as well as size, topography and land use of the respective catchment. These indices are assumed to be related both to water quality as well as to biological issues of the kettle holes. Starting in the mid-1990s, an extensive monitoring program has been established in the federal state of Brandenburg, Germany. In this study, a subset comprising 1,316 samples from 79 kettle holes was analysed, where 21 parameters had been determined. Sampling intervals varied widely, and were between bi-weekly and three-monthly at most sites. A nonlinear principal component analysis was performed. The first four components explained 90% of the variance. These components seem to provide quantitative measures of phosphorus release from the sediments during hypoxic periods, agricultural solute input, algae primary production, and geogenic compounds. This allowed differentiating between the natural and anthropogenic impact factors on water quality. In addition, scores of single components were related to properties of the kettle holes and their environments. The results contribute to a better understanding of biological and biogeochemical processes and can be used to verify the effects of conservation and management strategies for kettle holes.