Fish from the Amazon Basin are affected by oscillations in the river water volume, which influences the diet of animal species. This study was aimed at evaluating seasonal variations in lipid content, fatty acid composition and nutritional profiles of five fish species from the Amazon Basin. The lipid contents of all fish species were observed to be lower in flood periods than in drought periods; Brachyplatystoma flavicans showed the largest variation (6.75–15.43 %) between these periods, while Colossoma macropomum showed no significant difference (p > 0.05). The fatty acid composition in the five fish species varied throughout seasonal periods; saturated fatty acid (SFA) contents decreased in flood periods, whereas polyunsaturated fatty acid (PUFA) contents significantly (p < 0.05) increased for all the species in the same period. Leporinus friderici showed the highest content of α‐linolenic acid, (LNA 14.86 mg g−1) and Colossoma macropomum presented the highest content of docosahexaenoic acid (DHA 26.13 mg g−1) in flood periods. Prochilodus nigricans showed the lowest content of arachidonic acid (AA) in both periods, while Brachyplatystoma flavicans showed the greatest amount of AA, 18.77 mg g−1 in drought period and 22.10 mg g−1 in flood period. All the fish species presented favorable indices of nutritional quality of lipid fraction, suggesting that consumption of these species could be considered beneficial to human health.