Aquaculture accounts for almost one-half of global fish consumption. Understanding the regional impact of climate fluctuations on aquaculture production thus is critical for the sustainability of this crucial food resource. The objective of this work was to understand the role of climate fluctuations and climate change in subtropical coastal estuarine environments within the context of aquaculture practices in He'eia Fishpond, O'ahu Island, Hawai'i. To the best of our knowledge, this was the first study of climate effects on traditional aquaculture systems in the Hawaiian Islands. Data from adjacent weather stations were analyzed together with in situ water quality instrument deployments spanning a 12-year period (November 2004 -November 2016). We found correlations between two periods with extremely high fish mortality at He'eia Fishpond (May and October 2009) and slackening trade winds in the week preceding each mortality event, as well as surface water temperatures elevated 2-3°C higher than the background periods (March-December 2009). We posit that the lack of trade wind-driven surface water mixing enhanced surface heating and stratification of the water column, leading to hypoxic conditions and stress on fish populations, which had limited ability to move within net pen enclosures. Elevated water temperature and interruption of trade winds previously have been linked to the onset of El Niño in Hawai'i. Our results provide empirical evidence regarding El Niño effects on the coastal ocean, which can inform resource management efforts about potential impact of climate variation on aquaculture production. Finally, we provide recommendations for reducing the impact of warming events on fishponds, as these events are predicted to increase in magnitude and frequency as a consequence of global warming.