Integrated assessment of ecological status and ecological well-being of water bodies based on monitoring presupposes attributions of the aquatic ecosystems to definite gradations of trophic state and level of pollution. In really these attributions are carried out by means of multi-criteria evaluation. The evaluation uses a number of parameters. Each of them must be indispensable, and the parameters taken together must be sufficient for the precise evaluation. Of course, each of the parameters must be suitable for the aquatic ecosystems monitoring. There are many parameters for the trophic state and the ecological well-being assessment. Thus, we can use several dozens of the characteristics for the trophic level estimation. For this reason, there are three interrelated problems. Firstly, the parameters may have non-equal significances. The next problem consists in the fact of probable differences in the parameters values changes with the same anthropogenic influence. Furthermore, there is problem of the values spatial and temporal variability. The dynamics may have different intensities. It is evident that natural researches of the problems demand too much time and money. Nevertheless, we have to determine the optimal scheme of the monitoring. Computer simulation of aquatic ecosystems functioning can help us with the determination. There is considered some results of numerical experiments with the computer model “EVTOX” of flowing water body ecosystem. The results present changes in the model components and processes with various anthropogenic impacts. In addition, there is discussed problem of intake of biogenic elements and pollutants into rivers from urbanized environment.