Most stock assessments and harvest strategies have an underlying assumption that the major driver of changes in populations is fishing pressure. This may not be valid for inland fisheries where environmental drivers are potentially of greater importance and there is a need to identify appropriate assessment and management approaches for use in this context. In this study we applied the FishPath harvest strategy development tool to five case-study fisheries within the Australian Murray-Darling Basin to compare possible assessment and management methods within a structured framework. These case studies included the only remaining commercial fishery (South Australian Lower Lakes), three riverine fisheries of varying water regulation and an impoundment fishery (Copeton Dam). Recreational fishing was the primary harvest activity in all fisheries except the Lower Lakes. While some differences in the most appropriate assessment and management methods were identified among the fisheries, it is suggested that population dynamic models (such as age-structured integrated models or production models) and multiple indicator methods (potentially including both biomass indices and environmental triggers) should be tested as the next step towards formalising assessment of inland systems. The exercise also highlighted some of the unique characteristics of inland fisheries, including variable reliance on stocking and water flow for recruitment and the impacts of large mortality events such as fish-kills which need careful consideration as part of assessment and management strategies.