Mesophotic reefs (>30 m) are increasingly recognised as important habitats for reef fishes and may act as depth refuges from shallow-water disturbances, including fishing. The deep reef refugia hypothesis was developed in relation to climate stress on coral reefs, but its application to fisheries is not well understood. This study aims to identify the demographic and ecological conditions under which deep habitat can function as a refuge from shallow-water fishing. We develop a spatial population model to simulate recruitment, growth, natural mortality, adult movement, and harvest across shallow and deep reefs. We then test how fishing mortality, deep-reef proportion, adult movement, and life histories interact to determine refuge benefits for fish populations and fisheries. Outputs identify the conditions under which spawning biomass remains above 20% and 40% of unfished levels, and compare catches between no-refuge and depth-refuge scenarios. Preliminary findings indicate that increasing deep-reef proportion raises spawning biomass, whereas adult exchange progressively erodes this protection. Refuge benefits are greatest for the most vulnerable life history under high fishing mortality. Compared with no-refuge scenarios, depth refuges may lower peak catches but potentially sustain relative catches across a broader range of fishing mortality. We then parameterise the model for Tasmania’s banded morwong fishery. This application is informed by new remotely operated vehicle (ROV) surveys of banded morwong abundance and acoustic tracking data on vertical adult movements. The outcomes complement an ongoing review of the current stock assessment model, which assumes that approximately 50% of the stock resides on deep reefs to seed shallow-reef fisheries productivity via larval dispersal, with a fixed annual adult exchange rate of 25%. By integrating new abundance and movement data, and accounting for heterogeneity in local reef area and deep-reef proportions, we assess whether existing stock assessment assumptions are adequate to estimate stock status and trends.