The River Murray estuary is the largest estuarine system in Australia, supporting a diversity of fish with varying biological and ecological traits. In recent history, the estuary has undergone dramatic fluctuations in environmental conditions (e.g. the Millennium Drought). However, there is little understanding of how these environmental fluctuations have affected the fish inhabiting the system. This study assessed responses in growth to decadal environmental variation including flow in species of fish with differing ecologies: golden perch (freshwater obligate), black bream (estuarine dependent), and mulloway (estuarine opportunist). Biochronologies based on otolith growth increment widths were developed for each species using a mixed modelling approach. Biochronologies, ranging 15 to 36 years and spanning a period of severe drought, showed considerable inter-annual variation in growth. Biochronologies were then correlated to a range of local and regional hydrological and atmospheric time series data at seasonal and annual temporal scales. Among species, environmental drivers of growth variation differed. River flow at the barrages near the Murray Mouth was found to be most influential in driving golden perch growth, while the growth of mulloway and black bream responded to fluctuating temperatures and local rainfall, respectively. These results suggest that generalisations about environmental influences on ecosystem functioning mask species-specific responses, as fish respond to environmental change dependent on the constraints of their life history strategies. These findings more broadly highlight the importance of considering the diversity of ecological groups that inhabit an ecosystem when developing conservation and management strategies.