Patterns of annual freshwater flows in the Murray River and recruitment of mulloway, Argyrosomus japonicus (Scianidae) were reviewed in terms of recent age structures and historical catches and CPUE. Age distributions from the nearshore marine fishery were dominated by the 1993 age class which comprised 35% and 41% of 2001 and 2002 catches, respectively. In 1993 annual freshwater inflow was 2.4 times the 25 year average. Freshwater inflow explained 28% and 35% of the variability in year class strength in the nearshore marine fishery in 2001 and 2002, respectively. Over 80% of the current South Australian commercial catch of mulloway comprises juveniles taken from the remnant estuary of the Murray River. Our results suggest that recent low levels of recruitment in South Australia's fisheries for A. japonicus may reflect low fresh water inflows since 1993. Since 2000, southern Australia has experienced the worst drought in recorded history and management strategies for this fishery must take into account effects of both environmental factors and fishing mortality on this vulnerable sciaenid population. We suggest that the population of A. japonicus located about the Murray River system is estuarine dependent, that the estuary provides important refuge for juveniles, and that strong year classes, or their absence, may be related to freshwater inflow to this environment. We also suggest that age distributions of this apex predator may provide an indicator of environmental health for the Murray River estuary.