Human activities have substantially altered fish populations through recreational and commercial harvest. These operations selectively remove individuals targeted by fishing gear, altering the size structure, and phenology of the remaining population. Simultaneously, aquatic ecosystems are further challenged by rapid environmental change and warming. Marine protected areas (MPAs) have been widely introduced worldwide as a conservation measure to help alleviate fishing pressure. While the impacts of MPAs on fish abundance and diversity have been well-studied, the changes to fish size-spectra and body size are poorly documented. Our study examined the size-spectra of fish communities across fished and unfished areas throughout Port Phillip Bay, an area heavily impacted by human activities and climate warming. We used stereo-baited remote underwater video surveys to assess local fish diversity, identify species, and measure individuals to compare how fish body size, as a proxy for growth, is impacted by fishing pressure. This work will contribute to our understanding of how MPAs can be utilized to protect the demography of important fish stocks and the thermal sensitivities of fished species as MPAs have great potential to be a management strategy that can increase species’ resilience to climate change.