Aquaculture is essential to Egypt's food and nutrition security, contributing over 1.5 million tonnes of fish annually, approximately 80% of the country's total fish production. However, the sector faces increasing risks from climate change and socio-economic transformations such as population growth, food demand, land-use dynamics, and governance shifts. Here, we adapt the GOMAP model for land-based systems to project aquaculture production potential (APP) under three Shared Socio-economic Pathways (SSP1–2.6, SSP2–4.5, SSP5–8.5) across five major governorates: Behera, Damietta, Kafr El-Sheikh, Ismailia and Port Said. Our analysis integrates species distribution models for key farmed fish species in Egypt, machine learning-based projections of pond water temperatures and the dietary demands of farmed species. Results indicate that under SSP1–2.6, most regions sustain or improve their APP through the 21st century, with governorates like Ismailia and Port Said maintaining 100% potential relative to the 2020s. In SSP2–4.5, however, APP becomes increasingly uneven; Behera and Kafr El-Sheikh decline by up to 79% and 74% respectively, by the 2090s, while Port Said and Ismailia retain higher resilience. Under SSP5–8.5, APP declines are most severe and widespread, especially for tilapia, with production potential falling below 50% in multiple regions by the end of the 21st century. Mullets and catfish show greater climate resilience across all scenarios. These findings highlight the urgent need for targeted adaptation strategies, including selective breeding, shading and aeration systems, and spatial reallocation to climatically stable regions. This modelling framework offers a valuable decision-support tool for ensuring sustainable and climate-resilient aquaculture development in Egypt.