Tropical reservoirs are sensitive to eutrophication but long-term impacts of impoundment on their productivity and biota are poorly understood. Here, we employ a palaeolimnological approach to assess whether ecological baselines can be defined for reservoirs, and examine the challenges and management implications. We studied the environmental history of five reservoirs in Brazil with different productivities, using sediment records covering the period since reservoir construction (~ 50–90 years). Our main goals, based on the analysis of organic geochemistry (TOC, TN, TP, C:N), stable isotopes (δ13C, δ15N), and diatoms, were to reconstruct and compare the magnitude of environmental changes, to determine the conditions prior to any eutrophication and discuss the implications for reservoir management. We inferred that Ribeirão do Campo reservoir has remained oligotrophic since its construction, Itupararanga and Paineiras have both remained mesotrophic with an improvement in water quality around 1970, and Salto Grande has been eutrophic since its construction in 1949. In Rio Grande reservoir, which was originally oligotrophic, eutrophication began in the 1950s, with a slight improvement in water quality after its separation from Billings Reservoir, followed by a subsequent decline in quality since ~ 2001. We found that the studied reservoirs have unique environmental histories and there are clearly challenges associated with defining ecological baselines for reservoirs against which the extent of degradation can be assessed. Nonetheless, when the data from all reservoirs were compared, a coherent pattern in the diatom assemblages emerged, reflecting the trophic gradient. The diatom assemblages prior to enrichment were composed of two groups. The oligotrophic baseline was characterized by several benthic species with low abundances, mainly Eunotia and Brachysira, while in three reservoirs the early assemblages were characterized by planktonic taxa associated with mesotrophic conditions, namely planktonic species Aulacoseira ambigua, Aulacoseira tenella, Discostella stelligera, and Spicaticriba rudis. This work provides information on the baseline conditions, the natural variability of non-degraded reservoirs, and the degree of ecological change in degraded ecosystems. This study contributes to an improved understanding of the timing and extent of eutrophication in these systems and provides information to help better inform the management of tropical reservoirs vulnerable to anthropogenic pressures
