The IPCC Special Report on Global Warming of 1.5 °C highlights the potential for dietary shifts to reduce greenhouse gas emissions from livestock. Reductions in the consumption of terrestrial animal protein require increases in the consumption of other food categories, to maintain food security, balanced dietary patterns, and protein intake. Aquaculture has long been suggested as one way to meet future food security needs, and marine and estuarine aquaculture in particular is associated with comparatively low greenhouse gas emissions. However, marine and freshwater aquaculture is affected by factors including harmful algal blooms (HABs), which have been increasingly documented around the world, correlated to increases in worldwide aquaculture. In this study, we applied a global multi-region input-output model to capture the direct effects as well as the indirect and induced effects HABs might pose to a global dietary transition from terrestrial livestock to increased seafood consumption from marine and estuarine aquaculture sources. We found that marine and estuarine aquaculture has a substantial potential to replace meat consumption from terrestrial livestock sources, as increases in CO2 emissions from aquaculture were more than offset by reductions in emissions from mainly cattle grazing and associated land clearing. HABs were found to have a minor monetary impact, but the impact on protein supply was found to be potentially sizeable. For example, in a future setting where 40% of terrestrial protein sources were replaced by aquaculture, a HAB-caused global loss of 5% would set in motion numerous supply-chain cascades, affecting industries auxiliary to aquaculture, indirectly and ultimately reducing protein intake by 10–20%. Such reductions have the potential for pushing parts of Sub-Saharan populations into protein-energy malnutrition. Nevertheless, there remains a significant potential for a dietary transition to increased aquaculture seafood to contribute to reductions in GHG.