Phosphorus (P) is an essential nutrient for life and thus one major driver for eutrophication of aquatic systems. Reduction in the P inputs via rivers should counteract a further rise in the nutrient level of the Baltic Sea. The extended P monitoring in the Warnow Estuary led to a better understanding of estuarine processes. The Warnow is a typical lowland river in northern Germany, discharging into the southern Baltic Sea. This work defines four operational P-fractions: dissolved molybdate-reactive P (DRP) and non-molybdate-reactive P (DNP) as well as particulate molybdate-reactive P (PRP) and non-molybdate-reactive P (PNP). Dissolved P is transformed into particulate P either by uptake and release via organisms, or by sorption to and from particles. The experiments result in the realization of the bioavailability of DRP, DNP and PRP which contribute to the primary production in the estuary. They are transformed into PNP, which is bound to the organisms. The calculated P loads verify the function as a sink of the estuary (total P retention by 24 - 37 %). The loads and their composition depend on the precipitation of the respective year. In dry years, the loads are under the target of the Baltic Sea Action Plan and dissolved P fractions are discharged into the Baltic Sea. Nevertheless, further reduction measures are necessary.