Generally, in water ecosystems, it is assumed that rivers play a transport role. In turn, lakes have accumulation properties. However, in fluvio-lacustrine systems, each water body located on a river track can disrupt naturally occurring processes. One such process is the nitrogen cycle. An analysis of the nitrogen cycle, at both the global and local levels, is of extreme significance in view of the progressive degradation of aquatic ecosystems. In this study, we attempted to show that the specific properties of reservoirs located in river–lake systems contribute to an adequate reaction of these reservoirs to situations involving an excessive pollution load. Despite the intensive exchange of water in lakes, they were mainly shown to have an accumulation function. In particular, in those located in the lower part of the system, the total nitrogen load transported outside the example reservoir decreased by 4.3%. The role of these reservoirs depends on the morphometric, hydrologic, and meteorological conditions. The actual loading of the water body was shown to be more than double the permitted critical loading. The creation of conditions similar to those occurring in river–lake systems by, for example, delaying the outflow of water, may favor the protection of surface water from the last element of the system, because this limits the transport of pollutants. This study of the functioning and evolution of lakes’ fluvio-lacustrine systems, including the balance of the nutrient load, enables the prediction of the aquatic ecosystem’s responses in the future and their changes.