We compared structural and functional changes in macrophyte species composition in softwater lakes with isoetids located along the southern shore of the Baltic Sea (NW Poland) in two time periods (1955–1959 and 2015–2020). The research aimed to determine the trend of changes in macrophyte composition influenced by fields and/or urban fabric, as land use. The land-use pressure measure referred to the volume of land occupied around the lake. In the second time period, the number of plant species in the lakes increased twofold (20 vs. 39), compared to the first period. The average values of species richness were statistically higher (p < 0.001) in the second period (15.7 vs. 8.6). The functional diversity of plants in the lakes revealed statistically significant differences in both periods compared. The FD Rao values calculated for plant life span, growth forms, and FD multi-traits were statistically higher in the second period (p < 0.001). Our findings revealed that the anthropogenic pressure on lakes over a period of 60 years caused a decrease in the share of sensitive species in macrophyte species composition (isoetids and mosses), but an increase in common plants with a completely different set of species functional traits. This is related to the environmental changes that occurred between the two periods studied. First of all, we noticed significant changes in the transparency (visibility) of the water. In the second period, the value of this trait is used in each lake, which uses the transmission of photosynthetic active radiation (PAR) light transmittance to the plant and can affect the species composition. These findings show that an increase in biodiversity can relate to a decrease in freshwater ecosystem function, mainly via lost function of evergreen isoetid species.