This paper presents the results of research into pathways leading to the production of methane (CH4) and carbon dioxide (CO2) in sediments of two eutrophic reservoirs (Maziarnia and Nielisz), located in south-eastern Poland. In seeking to identify the pathways in question, use was made of analysis of stable carbon isotopes in CH4 and CO2 dissolved in pore water. This determined that CH4 is mainly produced through acetate fermentation, though the hydrogenotrophic methanogenic process may also be of importance, especially in deeper layers of sediments. Both the presence of autochthonous organic matter and increased pH values are shown to favour acetate fermentation. In turn, methanogenesis in sediments is assessed as capable of accounting for the generation of a considerable amount of CO2. Indeed, the role of methanogenesis in CO2 production is increasingly important further down in the layers of sediment, where allochthonous organic matter is predominant.