Estuaries in the Mediterranean climate regions of southern Australia are vulnerable to the effects of anthropogenic pressures and climate change. Many of these systems are affected by eutrophication, water extraction, increased loading of fine sediments and organic matter, hydrological modification, and altered geomorphology and connectivity. In many cases these human pressures are exacerbated by significant declines in freshwater flows under a drying and warming climate. The effects of these pressures are manifested as altered environmental conditions, which can act as stressors of estuarine fauna such as fish. We provide a series of case studies to highlight the key environmental stressors that shape fish communities in the estuaries of southern Australia, including altered salinity regimes, harmful algal blooms, reduced hydrological connectivity and environmental hypoxia. The impacts of these stressors range from shifts in community structure and functional guilds to the loss of particular species, and in extreme cases, mass mortalities (‘fish kills’). Although the literature documenting the ecological effects of these stressors continues to grow, in many cases our understanding of the mechanistic pathways between altered physico-chemical conditions and community-level effects remains limited. This uncertainty highlights the need to more effectively trace stressor impacts through various levels of biological organisation, from direct effects on the physiology, behaviour and biological performance of individuals, to consequent changes in population dynamics and, ultimately, community structure and function.