The Bay of Quinte is a large (254 km²) embayment on Lake Ontario, which has experienced many environmental and ecological modifications since the arrival of European settlers. Extensive clearing of land and development of urban areas led to considerable eutrophication from anthropogenic nutrient loading in the late 1800s. The subsequent reduction of nutrient loading post-1977 was followed by the 1994 colonization of invasive dreissenid mussels, whose establishment was associated with benthification and an abrupt shift from a turbid eutrophic system to a clearer mesotrophic system. To investigate the response of the benthos to these stresses, a sediment core was collected in 2023, and sediment subsamples from 18 stratigraphic intervals were sifted to identify and enumerate subfossil chironomid (order: Diptera) assemblages. The cultural eutrophication of the bay was reflected in the sediment core by a shift from hypoxia-intolerant Tanytarsus lugens and T. mendax dominance to the more tolerant Chironomus sp. After 1977, Chironomus sp. decreased and Tanytarsus spp. and other hypoxia-intolerant taxa increased, consistent with nutrient abatement actions. Following dreissenid establishment (∼1994), there was a significant increase in chironomid head capsule abundance. ANOSIM suggests that the nutrient abatement actions may be a stronger driver of chironomid taxonomic and functional composition than the dreissenid invasion, though this may reflect the resolution and location of the sediment core. Overall, our results suggest chironomids experienced recovery from eutrophication and that benthic resource availability may have increased post-dreissenid invasion, which could benefit benthivorous fish.