The global demand for energy underscores the necessity of developing advanced and sustainable enhanced oil recovery (EOR) techniques to the trapped residual oil in mature carbonate reservoirs. While nanotechnology and engineered low water flooding have individually demonstrated potential in altering rock wettability and reducing interfacial tension (IFT), their synergistic combination remains underexplored, particularly for creating strongly hydrophilic conditions. This study designs and synthesizes a novel carbon-based nanocomposite low salinity water system, integrating graphitic carbon nitride (g-C3N4) nanoparticles with zirconia (ZrO2) nanosheets to form a stable, high-surface-area composite dispersed in tailored low-salinity water. The developed nanofluid is comprehensively characterized using XRD, FTIR, BET, TEM, TGA, zeta potential, conductivity, contact angle, IFT, adsorption, and core flooding experiments. Results indicate superior performance, with IFT reduced from 28 to 2.65 mN/m and contact angle decreased from 146° to 32.5°, confirming a significant shift towards water-wet conditions. Core flooding tests demonstrated an additional 31% recovery of original oil in place beyond conventional low-salinity water flooding. The study provides a detailed mechanistic analysis, revealing that the synergy between the nanocomposite and low-salinity water enhances disjoining pressure, stabilizes the nanofluid via increased negative zeta potential (-49.87 mV), and optimizes adsorption onto carbonate surfaces. This work presents a novel, economically viable nanofluid strategy that advances enhanced oil recovery technologies by offering a potent solution for improving recovery in carbonate porous media. The estimated chemical cost of this approach is $0.036–0.084 per barrel of injected fluid at 240 ppm.