•An improved reinforced concrete steel bar deterioration model that incorporates pitting corrosion is proposed.•Change in after-cracking corrosion rate is considered to assess the time-dependent seismic fragility of RC bridges.•Differences in the results when reinforcing steel is subjected to general and pitting corrosion are investigated.•Seismic fragility of deteriorating RC bridges in marine environment is evaluated. This paper presents an improved reinforced concrete steel bar deterioration model that incorporates pitting corrosion and considers the change in after-cracking corrosion rate to assess the time-dependent seismic fragility of RC bridge substructures in marine environments. The proposed deterioration model is applicable for both existing and new RC bridge substructures and could be employed for life-cycle analysis of RC bridge substructures in marine environments. In this paper, the model is implemented to conduct a probabilistic seismic fragility analysis of a three-span continuous box girder bridge accounting for uncertainties in establishing bridge geometry, material properties, ground motion and corrosion parameters. Differences in the results obtained when reinforcing steel is subjected to general and pitting corrosion are investigated. The results show that the effect of chloride-induced corrosion cannot be neglected when performing the seismic fragility analysis of RC bridge substructures in marine environments. Additionally, the calculated time-dependent fragility curves indicate that there is a nonlinear accelerated growth of RC column vulnerability along the service life of highway bridges, especially after twenty-five years of exposure to chlorides.