Concrete containing metakaolin (MK) and ternary blends of MK and fly ash (FA) were prepared. A long-term exposure experiment at in-situ marine splash zone for the prepared concretes were carried out. Total and free chloride content of the exposed concretes were tested. SEM-EDS was used to analyze the morphology and element composition of the hydrates, while XRD was used to determine the phase component of the exposed concretes. The results show that the chloride content and chloride diffusion coefficient of concrete under actual marine environment are decreased with the application of MK, while the chloride binding capacity is enhanced. The improvement effect becomes more significant when FA is applied in the MK concrete. A denser structure of concrete can be obtained by the use of MK. Higher A/S and lower alkalinity of the hydrates of MK concretes promote the formation of Friedel’s salt. In addition, the application of MK did not have detrimental effect on sulfate resistance of the long-term exposed concretes.