The macro-litter (plastic) sea bottom pollution of 14 city harbors and marinas in North Africa and in the western Baltic Sea was investigated using a new simple mobile underwater camera system. The study was complemented by a harbor manager survey and 3D-hydrodynamic transport simulations. The average pollution in German marinas was 0.1 particles/m² sea floor (0.04–1.75). The pollution in North African marinas on average was 7 times higher (0.7 particles/m²) and exceeded 3 particles/m² in city center harbors. The resulting >100,000 litter particles per harbor indicate the existence of a problem. With 73%-74%, plastic particles are dominating. Existing legal and management frameworks explain the lack of plastic bottles and bags on sea floors in Germany and are one reason for the lower pollution levels. Items that indicate the role of untreated sewage water were not found. Harbor festivals seem not to be quantitatively relevant for open sea bottom pollution. Our method tends to underestimate the pollution level. Model simulations indicate that storms can cause litter reallocations and sediment cleanings. However, marina sea floor monitoring is recommendable, because it addresses pollution hot-spots, is cost-effective and takes place close to emission sources. Further, the effectiveness of land-based pollution reduction measures can easily be assessed.