Abstract Multivariate patterns in commercial fisheries landings, effort and revenue from three adjacent estuarine and coastal systems were examined in eastern Australia between 9-month periods of flood (September 2000–May 2001) and drought (September 2002–May 2003). Patterns in species landings, methods of fishing effort and revenue per species were significantly different between flood and drought. Spearman’s rank correlations between Bray–Curtis similarity matrices for landings, effort and revenue indicated that patterns in fisheries metrics represented a mixed signal of ecological response and fishers’ harvesting behaviour. Flood and drought events were associated with shifts in the species composition of landings that were reciprocated between estuarine and coastal systems. Estuarine migrant species (e.g. school prawn Metapenaeus macleayi Haswell) primarily contributed to landings during flood, whilst marine estuarine-opportunist species (e.g. yellowfin bream Acanthopagrus australis Owen) primarily contributed to landings during drought. Flood and drought events redistributed fisheries resources between estuarine and coastal systems, modifying the bioeconomic productivity of commercial fisheries. Results indicated that flood and drought events influence commercial fisheries by modifying landings composition, fishers’ harvesting behaviour and revenue generation.