Determining the impacts of non-fishing effects on stock abundance is an ongoing challenge within fisheries stock assessment and has implications for fishery management. Such effects can include large scale oceanographic processes such as the El Niño-Southern Oscillation (ENSO) which have been shown to influence trends in recruitment in a range of species. In South Australia, large fluctuations in the catch of Penaeus (Melicertus) latisulcatus from the West Coast Prawn Fishery (WCPF) have been observed, particularly following El Niño events. The challenge has been in differentiating between environmentally and fishery-driven changes in biomass or distribution patterns. Recently, a draft harvest strategy has been developed for the WCPF with performance indicators and reference points developed that for the first time take into account El Niño events. The key performance indicators are total prawn abundance, calculated from commercial and fishery-independent survey CPUE, and ENSO status which identifies a recent El Niño event. The proposed decision rules allow for more moderate effort reductions for one year following an identified El Niño event. Addition of this feature in the harvest strategy aims to sustainably manage the WCPF through future El Niño events.