AbstractDespite continued calls for the application of ecosystem‐based fisheries management, tactical fisheries management continues to be heavily reliant on single‐species stock assessments. These stock assessments rarely quantitatively integrate the effects of ecosystem processes on fish stock productivity. This lack of integration is ultimately driven by the complexity of interactions between populations, ecosystems and fisheries, which produces uncertainty when defining which processes to include and how to include them. Models developed using a structured hypothesis testing framework would allow formalizing uncertainties while underscoring the importance of incorporating different population and ecosystem processes to explain non‐stationary stock productivity. Here, we develop a conceptual framework for extending and comparing population dynamics models of increasing complexity. We illustrate the utility of the framework by investigating the population and ecosystem processes that most likely affected the differential recovery of two flatfish populations (American plaice and yellowtail flounder) on the Newfoundland Grand Banks over the past three decades. We found that yellowtail flounder population dynamics were primarily driven by recruitment variability, which was negatively affected by warmer climatological conditions, as indicated by an integrated regional climate index. Meanwhile, American plaice population dynamics were affected by a combination of temporal variability in recruitment and natural mortality, where natural mortality increased during colder than average conditions. By exploring hypotheses about the effects of population and ecosystem processes on population dynamics, this modelling framework will improve understanding about the drivers of shifts in population productivity while serving as a transparent and robust approach to support ecosystem‐based fisheries management.