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Solea senegalensis is a commercial flat fish traditionally farmed in earth ponds in coastal wetlands that might also become important to more intensive aquaculture. Gas bubble disease (GBD) is a potential risk for outdoor fish farming, particularly in certain periods of the year, related to improper management leading to macroalgae blooms. Physical-chemical conditions inducing hyperoxia, including radiation, temperature, and high levels of dissolved oxygen, have been monitored in fish affected by GBD together with observed symptoms. Exophthalmia, subcutaneous emphysemas, obstruction of gill lamellae, hemorrhages, and anomalous swimming were the main effects of oxygen supersaturation. A proteomic study was carried out for the first time under aquaculture conditions and protein expression changes are described for fish that were subject to hyperoxic conditions. Proteins identified in gill of GBD-affected fish are related to oxidative alteration of cytoskeleton structure/function (beta-tubulin, beta-actin), motility (light myosin chain, alpha-tropomyosin), or regulatory pathways (calmodulin, Raf kinase inhibitor protein), reflecting the central role of gill in oxygen exchange. Hepatic proteins identified are related to protein oxidative damages (beta-globin, FABPs), protection from oxidative stress (DCXR, GNMT), and inflammatory response (C3), in agreement with the predominant metabolic role of liver. Comparison of protein expression patterns and protein identification are suggested as potentially specific hyperoxia biomarkers that would facilitate prevention of GBD outbreaks.