Stable isotope analysis has become a powerful tool for the study of food web structures in aquatic communities. However, there has been little recognition of the spatial and temporal variabilities of isotopes in food webs in peatbogs. Here, we investigated the structure of food web in peatbog dominated by Sphagnum mosses by analyzing: (i) density and biomass of different components of food webs; (ii) the digestive vacuole contents of Hyalosphenia papilio—the most abundant species of amoebae occurring in peatbog; (iii) the seasonal changes in the carbon and nitrogen stable isotope signatures of particular components of food web. The study was performed in the Moszne peatbog located in the western part of Polesie Lubelskie (eastern Poland). Fieldwork was done on a monthly basis from April to November 2013. The largest total biomass of microorganisms in all of the seasons was noted in testate amoebae. Algae and cyanobacteria were the second largest group of microorganisms. The feeding behaviour of H. papilio varied throughout season. Among the identified prey, the highest frequency was noted in algae, cyanobacteria and ciliates. In spring and summer, prey was dominated by phycoflora, while during the autumn period the main prey consisted of cyanobacteria and ciliates. The results of the study indicate significant seasonal variation in the level of stable isotopes in individual components (bacteria, fungi, protozoa and metazoa) of the food web of peatbog, and thus also considerable dynamics of changes between trophic levels.