Aquaculture accounts for almost one-half of global fish consumption. U nderstanding the effects of climate fluctuations and climate change on aquaculture is therefore critical for the sustainability of this important food resource . Our objective was to understand the role of the 2009 El Niño in tropical coastal estuarine environments with in the context of aquaculture practices in Heʻeia Fishpond, Oʻahu Island, Hawaiʻi . This was the first study examining climate effects on traditional aquaculture systems in the Hawaiian Islands. Data from two adjacent weather stations were analyzed with in situ water quality instrument deployments spanning a 12-year period (November 2004 - November 2015 ). We found correlations between two periods (May and October 2009) with extremely high fish mortality (i.e., 'fish kills') at Heʻeia Fishpond and slackening trade winds in the week preceding each fish kill event, as well as elevated sea surface temperatures (SST) 2-3 °C higher than background periods ( March-December 2009). We posit that lack of trade wind driven surface water mixing promoted enhanced surface heating and stratification of the water column, leading to hypoxic conditions and stress on fish populations. The impact on fish was amplified because the fish were contained within net pen enclosures. Elevated SST and interruption of trade winds have been previously linked to the onset of El Niño in Hawaiʻi. Our results provide empirical evidence regarding El Niño effects on the coastal ocean, as well as on aquaculture . These findings have informed resource management efforts about potential impact of climate variation on aquaculture production.