Nanomaterials have received increased concentration in the field of civil engineering, as their incorporation can effectively modify the mechanical and transport properties of cementitious composites. In this study, to understand the effect of graphene oxide (GO) nanoparticles on the durability and mechanical properties of cementitious composites serving underwater, mortars incorporated with GO were taken for study. To match the real circumstance, all specimens were immersed directly in a flowing river for three years, and their transport properties, mechanical properties and microstructure before, and after, river experience were studied separately. The results showed that the incorporation of GO could reduce both early-age permeation coefficient and later-age chloride migration coefficient of mortar specimens. The average porosities of mortars could be reduced by the range of 3.37–11% with GO incorporation. Moreover, through a novel dual-scan method, GO incorporation was confirmed effective in enhancing both the leaching and cracking resistance. Furthermore, the compressive strengths, flexural strengths and splitting tensile strengths could be improved by the range of 4.37–9.82%, 7.78–22.33%, 8.14–28.73%, respectively with GO incorporation, and the tested mechanical strengths for GO-incorporated mortar after three-year river experience could be retained to a higher extent. Finally, based on durability and mechanical properties, the optimum mix proportion of GO was determined to be 0.06 wt.% in this study. The work presented here is of high reference value for the designing of marine infrastructure and can help promote the application of nanomaterials in civil engineering.