The fishery-dependent data used to estimate fishing production technologies are shaped by the incentive structures that influence fishermen’s purposeful choices across their multiple margins of production. Using a combination of analytical and simulation methods, we demonstrate how market prices and regulatory institutions influence a dominant short-run margin of production—the deployment of fishing time over space. We show that institutionally driven spatial selection leads to only a partial exploration of the full production set, yielding poorly identified estimates of production possibilities outside of the institutionally dependent status quo. The implication is that many estimated fisheries production functions suffer from a lack of policy invariance and may yield misleading predictions for even the most short-run of policy evaluation tasks. Our findings suggest that accurate assessment of the impacts of a policy intervention requires a description of the fishing production process that is sufficiently structural so as to be invariant to institutional changes.