In the middle of the last century in the case of many river basins, it became obvious that the targets of the Helsinki-Commission (HELCOM) concerning a 50% reduction of nitrogen and phosphorus inputs to the Baltic Sea had not been reached. Such conclusions could be derived from the observed loads. But the measurements regarding the analysis were not sufficient to determine what the reasons for this report were, what has to be done to fulfil this agreement and to evaluate the time at which the targets can be reached. This contribution presents the current state of Polish surface water quality as well as results of modelling nutrient and heavy metal emissions into the two biggest Polish river basins: Vistula and Odra, which both cover approximately 90% of Poland's territory.