Urban water courses are considerably degraded in terms of their hydrology, riparian and channel morphology, substrate heterogeneity and habitat features as well as water and sediment quality. In addition, the combined sewer overflows and the ecotoxicological impacts of its components lead to a change of the physical-chemical and microbial mass balance affecting the biocenoses of higher trophic levels. Combined sewer overflows are therefore an additional stress to the ecological status of the urban course of the River Spree and of its channels, which is damaged already by both preload and background load of the aquatic environment. With regard to the assessment of the ecological water status, the European Water Framework Directives gives priority to the aquatic biocenoses in their capacity as ecological quality parameters. Against this background, an immission-oriented approach for the assessment of combined sewer overflows has to describe also their impacts on the biocenoses of the macrozoobenthos, the fish fauna, the macrophytes and the phytoplancton. Initially, the most important factors, mechanisms and processes determining the mass balance of a water course are described. Particular attention is given to the mass balance of eutrophic lowland streams and rivers and of river-lake–systems. In this context, the abiotic mass balance is discussed together with the biotic use of resources. After introducing the basic processes of the mass balance, the impacts of the anthropogenic use on these processes are subsequently described with regard to Berlin’s specific water resources environment. The result is a compilation of the hydraulic, physical-chemical and ecological parameters relevant to Berlin’s water resources serving for water quality assessment purposes. Starting from the ecological processes disturbed by the anthropogenic use, the potential effects of the combined sewer overflow are examined. The parameters selection is concentrated on the essential processes connected to combined sewer overflow issues. Based on the large number of stress factors and their interactive impact system, those influences of the combined sewer discharge are worked out which have to be categorised as particularly jeopardising and which are important target values for the future water quality simulation. Due to the high background load, the highest priority has to be given to the acute load caused by nutrients and carbon load peaks resulting from combined sewer discharges, since they overcharge the self-cleaning potential of the urban course of the River Spree and its channels. Even if the organic substances and the chemical contaminants discharged lead to chronic loads, the main objective is to avoid to the greatest possible extent the temporary but extremely hypoxic conditions, since combined sewer overflows cause fish die-offs when the water resources situation is already critical. Primarily, the water quality modelling has to be concentrated on the realistic mapping of the highly dissolved concentration charts of the target parameters oxygen and ammonia, since the degree of the biocenoses’ damage is rather determined through discharge duration, discharge intensity and frequency than through the medium rates of pollutant loads.