Food web theory predicts that one of the consequences of oligotrophication is the decline in fisheries following the establishment of nutrient-deficient conditions and low biogenic production. However, emerging evidence suggests that more complex trophic interactions, induced by plankton composition, dietary diversification, temporal and spatial heterogeneity, variations in fish age and size structure can lead to ecosystem responses that deviate from theoretical predictions; especially in the shallow littoral zone. In this study, two end-to-end modelling strategies are used to characterize potential food web structural shifts and overall ecosystem productivity in response to oligotrophication. Our modelling strategy draws upon empirical and theoretical evidence from the Bay of Quinte, a semi-enclosed embayment in northeastern Lake Ontario that has been subjected to phosphorus (P) abatement strategies in the 1970s. We first show that the role of food abundance has been a primary factor shaping fish production, but the fish community gradually responded to the reduced availability of pelagic staples of their diet by displaying greater reliance upon alternative sources, including benthic and other autochthonous (or even allochthonous) food items. Our analysis further suggests that degree of diet overlap between competing trophic guilds can significantly modulate realized biomass levels. The composition of the autotrophic community is another major confounding factor that can induce significant variations from the predicted food web productivity patterns in response to oligotrophication. Overall, our analysis suggests that the proposed reduction of the ambient total phosphorus levels may not necessarily trigger a significant decline in fish biomass in the Bay of Quinte.