Autotrophic lakes are regarded to function as net autotrophic systems in which mobilization of solar energy by phytoplankton, benthic algae, and macrophytes forms the base of primary production. However, they are also subsided by allochthonous inputs. In this paper, we tested three hypotheses explaining the role of allochthonous subsidies as a driving force of autotrophic, bacterial, and heterotrophic production. The studies for this paper were conducted every fortnight from November 2015 to October 2017 in a small, shallow, temperate, eutrophic lake supplied with waters from four streams and drained by a single outlet. Changes in plankton biomass as well as variations in environmental conditions were estimated on the basis of the samples and measurements collected vertically in the water column (every 0.5 m depth) in the central part of the lake. Loads of nutrients and organic and inorganic matter were measured in both the inlets and the outlet of the lake, and on the basis of the differences between input and output loading, the amount of allochthonous subsidies in the lake was computed. Allochthonous subsidies affected the autotrophic production directly by supplying assimilable nutrients, and indirectly by providing allochthonous organic matter that supplemented the diet of omnivores and thus hampered their grazing pressure on phytoplankton. Bacterioplankton utilized allochthonous organic matter as well as effectively competed with phytoplankton for allochthonous nutrients. Dominant species of heterotrophic plankton were feeding opportunists, and thus inputs of allochthonous subsidies indubitably fostered high biomass of these species in the periods of low availability of autochthonous sources of food. Our finding suggests that allochthonous subsidies significantly affect trophic structure and impact both autotrophic and heterotrophic mobilization of energy through food chains in freshwater ecosystems.