Alkaline stress is a major concern in aquaculture that badly affects the aquatic species’ health and hemostasis. This research investigated the effect of carbonate alkalinity exposure on the gills and kidney organs as important organs for hemostasis, as well as the ameliorative role of camel protein hydrolysates (CPH) as dietary additives against alkaline stress detrimental impacts in Nile tilapia (Oreochromis niloticus). The fish (n = 160) were divided into four groups (G1, G2, G3, and G4), with the control (G1) fed a basal diet, while G2 was fed a basal diet supplemented with 75 g CPH/kg and was reared in freshwater (carbonate alkalinity of 1.4 µmol/L, pH = 7.19). The G3 and G4 were reared in alkaline water (carbonate alkalinity of 23.8 µmol/L, pH = 8.65) and fed the same diets as G1 and G2 for 30 days, respectively. The fish were stocked under a water temperature of 26.4 ± 1.5 °C, and the diets were introduced to the fish three times daily at a rate of 4% of their body weight. The results of this research showed that alkaline exposure increased kidney function parameters (creatinine, urea, and uric acid), glucose, and cortisol levels in the exposed fish. Alkaline exposure reduced the blood electrolytes level (calcium, magnesium, sodium, potassium, and chloride) and branchial antioxidant enzymes (superoxide dismutase, catalase, glutathione peroxidase, and reduced glutathione) and elevated malondialdehyde level in the exposed fish. Significant downregulation of the branchial expression of Na+/K+ ATPase α-3 subunit (0.17-fold), calcium/calmodulin-dependant protein kinase 1 β (0.23 fold), chloride channel protein 2 (0.38-fold), solute carrier family 12 a 2 (0.33-fold), and solute carrier family 4 a 4 (0.21-fold) was in the fish-reared under carbonate alkalinity stress. Alkaline exposure induced severe histopathological changes in the gills and kidney tissue architecture including inflammatory, circulatory, degenerative, and progressive responses. Supplementation of the Nile tilapia diet with 75 g CPH/kg ameliorated renal function and balanced the blood electrolytes, glucose, and cortisol levels in the alkaline-exposed fish. Modulation of the branchial gene expression profile and improving the gills and kidney microstructure were consequences of feeding on CPH diets during alkaline stress situations. Overall, fortifying the Nile tilapia diets with 75 g CPH/kg helps the fish restore their hemostasis and metabolic status during alkaline stress exposure which enables the sustainable culture of this species in such conditions.