We investigated the paleolimnology of Owasco and Seneca Lakes (New York, USA) and compiled water-quality monitoring data to describe environmental change during the past two centuries. Trophic shifts were detected in the oligotrophic to mesotrophic range and were likely driven by nutrient loading and species invasion. Based on box core reconstructions, primary production increased in both lakes during the last century, which is evidenced by the amount, type and isotopic composition of material preserved in the sediment. Organic matter accumulation and its stable carbon isotopic composition, as well as carbonate abundance, began to increase during the 1960s in Owasco Lake and the 1850s in Seneca Lake. Further, the abundance of phytoplanktivorous cladocera subfossils increased beginning in the 1910s in Seneca Lake and in the 1960s in Owasco Lake. The different timing and magnitude of the trophic shifts likely resulted from contrasts in lake residence time and species assemblages between the two lakes. The increases in primary and secondary production paralleled, and are interpreted to reflect, increased allochthonous nutrient loading. However, nutrient loading was not detected in the water-quality data, perhaps because of strong uptake of phosphates by phytoplankton or due to limited data collection. Rapid changes in cladoceran subfossils and water quality were also detected during the last decade. Concurrent with the establishment of non-native Cercopagis pengoi (fishhook waterflea), phytoplanktivorous cladocera remains declined, and the mucrone length of Bosmina increased, consistent with predictions of increased invertebrate predation. Additionally, the post-1990 decline in sediment carbonate, increased Secchi depth and decreased chlorophyll a concentrations followed the establishment of filter-feeding Dreissena spp. (zebra and quagga mussels). Collectively, paleolimnological data and water-quality monitoring provided a more complete and consistent record of shifts in the productivity of Owasco and Seneca Lakes, which were useful to understand environmental changes over different time scales. Physical, geochemical and biological changes were temporally consistent among three cores collected from different locations in each lake, but differed in magnitude for several variables (e.g., grain size and cladoceran subfossils), which could reflect near-shore to offshore gradients.