A critical component of science-based fisheries policy is the provision of habitat adequate for population renewal. Yet, the Fisheries Act of Canada pays little attention to managing fish habitat and was weakened by changes enacted in 2012. Specifically, determining the habitat’s role in contributing to fisheries is challenging when many stocks have severely declined. Based on three independent case studies, we show substantial declines in juvenile cod and pollock in coastal habitats across Atlantic Canada coinciding with declines in adult stocks. However, juvenile fish are still around and could aid in stock recovery. Thus, we recommend enhanced legislation for fish habitat management, particularly in valuing its potential for fish stock recovery.