This study aimed to evaluate appropriate water sources to improve Solea aegyptiaca aquaculture from larval to the juvenile stage using two water sources (Eastern Harbour (EH) and MaxWell (MW)). Firstly, four microalgae's nutritional value (Nannochloropsis salina, N. oculata, Chlorella salina and Tetraselmis chuii) was assessed in both water sources. MW of high nitrate content enhanced the algal biomass and biochemical composition of all species compared to EH. MW-N. salina showed the highest growth and biochemical contents among the investigated species and yielded Artemia franciscana with a considerable amount of arachidonic acid (ARA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) compared to EH. Secondly, Artemia enriched MW-N salina was used to improve S. aegyptiaca quality in both water sources from 10-48 days posthatch at a density of 15 larvae L −1. The MW-S. aegyptiaca exhibited a significant increase in morphometric parameters, albino percentages and recorded the highest ARA, EPA and DHA content (35.9, 6.1 and 15.9 µg g −1 , respectively) compared to that reared on EH. The study reports evidence of albinism of MW-S. aegyptiaca due to high dietary and ARA content. Overall, the seawater source has a significant impact on the whole food chain quality from microalgae to S. aegyptiaca.