Fears of food insecurity are a reality for vulnerable island nations and coastal communities, especially with impending climatic and environmental disasters. The 2020 breakout of SARS-CoV-2 further highlighted fundamental problems with the current centralized food system, inspiring more people to value local, community-produced options. Restoring indigenous aquaculture systems, such as Pacific Northwest clam gardens and Hawaiian loko iʻa (fishponds), holds great promise in helping small coastal communities adapt to a changing climate. Their integrated, low trophic level models increase natural seafood production without feeds or antibiotics. In turn, they increase the health of their surrounding ecosystem as well as the physical and mental health of those who utilize them. To do so, the systems rely on hyper-local traditional ecological knowledge (TEK) accumulated over centuries. But indigenous aquaculture is only a solution if it can function in climate change. Here we explore how the TEK embedded in indigenous aquaculture can withstand climate changes, while helping communities adapt to and mitigate the associated challenges.