This study presented the difference in the sediments under a large gap formed by the Durian typhoon in 2006 and its surrounding intact forest in Can Gio Mangrove Biosphere Reserve, Vietnam. Twelve plots previously settled in the original gap and its surrounding forest were used to collect sediments in the dry and wet season in 2019 to assess the difference in sediment properties and nutritional state caused by the self-recovery of the vegetation. Sediment temperature and pH were measured in field, while the contents of total organic carbon (Corg) and total nitrogen (Ntot) were subsequently quantified in the chemical laboratory. Sediment temperature, salinity, and pH between the gap and the surrounding forest were not statistically different. The variation of Corg concentration in the gap sediments seemingly increased with depth from 1–15 cm in the dry season. The Ntot in the gap sediments showed that it was continuously consumed in the underlying sediments during both seasons. In conclusion, the variation in vegetation composition between the gap and its surrounding forest was responsible for the differences in sediment C and N concentrations.