The present study explored the nutritional composition, phytochemicals analysis, and antioxidant capacity of two indigenous varieties of red and green water chestnut (WCN) fruit grown in Pakistan. Accordingly, this study was designed to investigate the proximate composition (moisture, ash, fiber, proteins, fat, and energy), physicochemical properties (pH, °Brix, and glycemic index), minerals, and vitamins. The methanolic extracts of WCN fruits were explored for phytochemicals (total phenolic and flavonoid content), and antioxidant potential was examined in vitro by 1,1-diphenyl-2-picrylhydrazyl radical scavenging capacity (DPPH) and Ferric reducing antioxidant power (FRAP). Quantitative determination of mineral (sodium, potassium, calcium, phosphorus, iron, manganese, copper, and zinc) and vitamin (vitamin C, vitamin B6, vitamin B2, vitamin B3, vitamin A, and β-Carotene) composition was also assessed. Based on the findings, the proximate compositions of WCN green and red varieties varied greatly as WCN green contained significantly higher protein (1.72%), fat (0.65%), dietary fiber (2.21%), moisture (70.23%), ash (1.16%), and energy content (112.8 Kcal) than WCN red. In WCN green, the macro–micromineral concentrations were significantly higher than WCN red. Among the minerals analyzed, potassium was the most abundant mineral found in both varieties. Levels of vitamin C, B6, A, and β-Carotene were significantly higher in WCN green. In this study, methanolic extract showed higher extraction efficiency than acetone, ethanol, and distilled water. WCN green had a significantly higher quantum of total phenolic (91.13 mg GAE/g) and total flavonoid (36.6 mg QE/g) and presented significantly higher antioxidant activity than the WCN red. This study showed that, among both varieties, WCN green extract has therapeutic potential against free radical mediated health conditions and suggested the potential use of this fruit as a source of natural antioxidants in nutraceuticals.