Decreased water levels due to climate change cause many negative effects on lake ecosystems. The aim of this study was to (a) assess the effect of the reduction of water levels on nutrient availability in the sediment in the littoral zone; (b) evaluate the effect of changes in water level on biomass productivity and nutrient concentrations in the aboveground biomass of four emergent species: Phragmites australis (Cav.) Trin. ex Steud., Typha angustifolia L., Carex acutiformis L., Glyceria maxima (C. Hartm.) Holmb; and (c) assess the efficiency of the littoral zone in the reduction of nutrient pollution. The study hypothesis was that water level reduction has a positive effect on the plant biomass of high productive species. The study was carried out in the littoral zone of Tomickie Lake, situated in the western part of Poland. This lake is located in the protected area—the buffer zone of Wielkopolska National Park, and at the international level—Natura 2000. Six transects, perpendicular to the shoreline, were selected at two subzones—permanently and seasonally flooded. Analyses of nutrient concentrations in sediments and plant species were performed. The results show the higher productivity of reeds in the zone where water occurs seasonally at the site through the year, which reached 1193 g dry weight/m2. The decline of the water level may lead to the increased growth of highly productive species as emergent vegetation with a broad ecological scale in terms of nutrient concentrations and changes of water depth, i.e., Phragmites australis (Cav.) Trin. ex Steud. Species that prefer growth in the deeper part of the lake will be characterized by lower productivity, despite the high availability of nutrients. Changes in the availability of nutrients may cause the intensification of lake overgrowth by very productive species, which may affect biodiversity, which is particularly high in protected areas.