Sustaining or improving native fish populations is a fundamental objective of many waterway management plans and interventions. While restoration projects usually occur over short time periods, changes to fish populations usually exceed this and often occurs at spatial scales beyond the footprint of the intervention. This misalignment through both time and space presents a challenge for managers and scientists, both for legislative requirements of evaluation and in the adaptive management space. We integrated more than two decades of fish monitoring data spanning mid-lowland reaches of 26 waterways across Victoria to assess long term trends in native fish abundance. We used a hierarchical Bayesian model to estimate trends in standardised fish catch through time, while also examining how these trends were influenced by a series of covariates. We present the high-level findings of our assessment along with detailed case studies specific to Murray Cod and Trout Cod populations across Victorian Rivers. These results have been used to assess native fish population dynamics across an expansive spatial and temporal scale, and by integrating complimentary research, enable more detailed assessments of the role of management interventions and broader climatic drivers in governing population trends.