The purpose of this study was to determine the biogas potential of biomass produced by microbiotic communities developed under natural conditions in freshwater systems such as ponds incorporated into agricultural landscapes. Natural communities of microalgae were collected from a small eutrophicated pond where dominant species were euglenoids (Lepocinclisspecies). Cyanobacterial communities dominated byLyngbyaspecies were taken from a domestic aquarium and cultivated under makeshift conditions. Experiments were done using dairy cow manure (DCM) for codigestion with natural communities of microalgae (MDM) and cyanobacteria (CDM) and conducted during 42 days in thermophilic regime. The total biogas yields were 421.40 and 383.34 mL/g volatile solids (VS), while the average methane contents were 63.97 and 64.06% for MDM and CDM, respectively. Our results indicate that the natural communities of microalgae and cyanobacteria used in this study possess the potential for biogas production, which is, in comparison with particular algal and cyanobacterial strains cultivated under strictly controlled cultivation conditions, more promising. Therefore, this study aims to motivate further investigations into the diverse natural communities of microalgae and cyanobacteria and pretreatments that are environmentally friendly and cost-effective and will eventually enhance small-scale biogas production on agricultural farms.