AbstractFisheries management strategies usually do not consider secondary consequences of environmental shocks. A recent viral disease outbreak that decimated blacklip abalone populations in southern Australia had a much smaller impact on the region's less‐abundant greenlip abalone populations. Decreases in total allowable commercial catch (TACC) for blacklip abalone were partially offset by a transient increase in greenlip abalone TACC that peaked in 2010 and reduced to zero in 2013. A hypothesis that the greenlip abalone stock had declined was supported by a Bayesian analysis of catch rates (catch per unit effort, CPUE, as a proxy for biomass). The estimated decline is consistent with depletion of the relatively small and fragmented greenlip stock as an indirect consequence of the disease impact. Our analysis demonstrates a need to jointly monitor and manage substitute fisheries when one of the fisheries experiences depletion as a result of a natural disturbance event.Considerations for Management Hierarchical Bayesian models can determine whether a shock to a natural resource indirectly affects related resources via a transfer of exploitation effort; Greenlip abalone stocks in western Victoria were generally poor in quality and infrequently exploited prior to the disease outbreak. Their low productivity rendered them vulnerable to the sudden increase in exploitation pressure, which could not be sustained once CPUE declined to 40–50 kg h−1, after which fishing activity ceased; A CPUE of 40 kg h−1 could be a precautionary limit reference point for triggering future greenlip abalone fishery closures; An increase in greenlip abalone legal minimum length (LML) to at least 140 mm would improve quality and profit; It is important to protect substitute resources from secondary exploitation when imposing restrictions on exploitation of resources that are adversely impacted by natural disturbance events.