The variation of a number of parameters characterizing aquatic plant assemblages in rivers across a wide trophic gradient was investigated to evaluate their usefulness for a Polish national river monitoring system. Analyses were conducted at 100 sites included in the national river monitoring system, representing a uniform river type, i.e., small- and medium-sized lowland rivers with a sandy substrate. Results of botanical surveys, which were supplemented with comprehensive monthly quality records, were obtained from the national monitoring database. By analyzing the Jaccard distances of the botanical metrics using the adonis function, the variation in species composition between rivers of different trophic status was determined. The group consisting of the most degraded rivers was the most homogeneous in terms of botanical composition. The cleanest rivers displayed a high level of heterogeneity within their group, as numerous different unique species were found there at low frequencies. The variation of the macrophyte metrics used to assess the ecological status (Macrophyte Index for Rivers (MIR) and River Macrophyte Nutrient Index (RMNI)) reflected a trophic gradient. We confirmed that vegetation diversification along a trophic gradient is evident enough to detect degradation in a five quality class system.