Ponds arising from groundwater in Cerrado of Central Brazil are oligotrophic but highly biodiverse environments. In this study, we used stable isotope ratios to test if there are variations in carbon and nitrogen acquisition by different primary food sources and if they are influenced by seasonality in a well-preserved pond. We hypothesized that periphyton is the main food source for macrophyte-associated fauna. We found that δ13C, but not δ15N, can distinguish between primary food sources; however, the isotopic signatures of food sources did not differ significantly between seasons. The δ15N values of macrophyte-associated fauna were significantly higher for predators compared with other trophic groups, but δ13C values did not differ significantly between groups. Emergent macrophytes and periphyton were the main food sources for scrapers (contribution of 42.5%) and collector-gatherers (contribution of 41.6%), respectively. Compared with emergent macrophytes, submerged macrophytes were associated with a greater abundance of fauna and algal biomass but were not a significant food source for associated fauna. Our findings demonstrate that in this small shallow oligotrophic pond in the Cerrado, the stable isotope ratios of carbon and nitrogen of food sources did not vary between seasons but did differ between aquatic macrophyte life forms. We point out the different functional roles of macrophyte life forms, with emergent macrophytes serving as an important food resource, while submerged macrophytes mainly provide physical structure.