According to the general classification of shallow eutrophic lakes, two alternative types are distinguished: phytoplankton-dominated and macrophyte-dominated lakes. The latter type is rare and currently endangered by human activity. In order to determine the effect of reduced inflow of surface water by an earth dyke on the lake trophic state, certain biological and physico-chemical parameters were evaluated. This work focuses on two lakes of similar morphometric characteristics situated in the agricultural landscape. The effect of the earth dyke on the trophic state was positively verified. The lake situated in the catchment basin, in which the inflow of surface water was reduced, was defined as meso-eutrophic, with a small amount of phytoplankton and high water transparency. The reference lake was highly eutrophic, with low water transparency and a large amount of phytoplankton. The water body surrounded by the earth dyke was macrophytes dominated (65% of the lake area), whereas the reference lake was a phytoplankton-macrophyte type (42% of the lake area). The trophic evaluation of a lake can be underestimated because of a significant amount of biogenic compounds accumulated in plant tissues. Thus, the values of Carlson’s indices in macrophyte-dominated lakes may not account for the total amount of nutrients in the water body.