The South Australian Marine Scalefish Fishery was traditionally managed through regulating fishing effort, which was supported by the use of bespoke, effort-conditioned integrated stock assessment models for key fishery species such as Southern Garfish (Hyporhamphus melanochir), King George Whiting (Sillaginodes punctatus) and Snapper (Chrysophrys auratus) developed over 20 years. In 2025, a new harvest management plan largely based on managing catch was implemented. This motivated the development of new Stock Synthesis stock assessment models for these key fishery species to estimate management quantities such as relative spawning biomass against reference points that then dictate recommended biological catch. Furthermore, South Australia was impacted by a major algal bloom in 2025 that led to mass fish mortalities and steep declines in catch per unit of effort for many species, leading to fishery closures and the interruption of commercial logbook data streams typically used in stock assessment models. This presentation will outline major research priorities and challenges associated with the development of new stock assessment models in the context of environmental change, and their use in fishery management. Possible options of bridging analyses between the Stock Synthesis and bespoke stock assessment models will be discussed, as well as the implementation of ecological catastrophes in integrated fishery models.