Soft water lakes with isoetids (SLI) are ecosystems prone to degradation due to the low buffer capacity of their waters. One of the main threats resulting from human impact is eutrophication due to agriculture, catchment urbanization and recreational use. In this paper, changes in the water chemistry and transformation of biocoenoses of one of the largest Polish SLI, Lake Jeleń, over the past 30 years are presented. The lake is located within the borders of a city, and a significant part of its catchment is under agriculture and recreation use. The physicochemical (concentration of nutrients, organic matter, electrical conductivity, oxygen saturation and water pH) and biological parameters (macrophytes and phytoplankton) were measured in summer 1991, 2004, 2013 and 2018. Since the beginning of the 1990s, a gradual increase in the trophy of the lake has been observed as indicated by increased nutrient availability, deterioration of oxygen conditions and a decrease in water transparency. The alterations of water chemistry induce biological transformations, in particular, an increase in phytoplankton abundance (4-fold increase of biomass in epilimnion) as well as a gradual reduction in the range of the phytolittoral (from 10 to 6 m), a decrease in the frequency of isoetids, Lobelia dortmanna and Isoetes lacustris, and expansion of plant species characteristic for eutrophy.