Typhoons frequently induce algal blooms in the open ocean based on the satellite remote sensing data. However, the effects of typhoons on nearshore areas are not fully clarified due to the inaccessibility of in situ sampled data and the low accuracy of satellite data in the nearshore areas. To understand the biogeochemical and ecological changes in semi‐enclosed bays under the influence of typhoons, physicochemical parameters and isotopic compositions of surface water were measured in Zhanjiang Bay during the super Typhoon Mujigae and nontyphoon periods. The results show that the chlorophyll a (Chl a) concentrations inside and outside the bay during these two periods were considerably different. During typhoon periods, the positive apparent oxygen utilization and unsaturated dissolved oxygen (DO) values suggested significant biological degradation in Zhanjiang Bay, rather than the algal blooms reported by previous studies. In contrast, during nontyphoon periods, particulate organic matter (POM: POC and PN) was mainly generated by in situ phytoplankton production, as indicated by a low POC/Chl a ratio (<99), low C/N ratio, and positive correlations between PN, POC, and Chl a. Isotopic analysis of the particulate N (PN) and nitrate (NO₃⁻) indicated that the ¹⁵N‐enriched PN in both periods originally came from sewage‐dissolved inorganic N. These results suggest that the typhoon‐induced decomposition processes, rather than algal blooms, in this semi‐enclosed bay in the northern South China Sea, providing new understanding of the impact of the typhoons on marine biogeochemistry and ecology.

The impact of typhoons on the ecology of the ocean has been observed using high‐accuracy satellite remote sensing data. However, few field observations in the ocean have been conducted to understand the effect of typhoons on the biogeochemistry because typhoon is furious, dangerous, and unpredictable. Here, we investigated the impact of Typhoon Wipha on the biogeochemistry of the coastal area of western Guangdong, northwest South China Sea. Our results show that the typhoon triggered phytoplankton blooms (the level of Chl a increased 3.25 times after the typhoon) nearshore (water depths <23 m); however, there was little change in the nutrients and Chl a offshore (water depths between 23 and 60 m). Terrestrial runoff and vertical seawater mixing were identified as the main processes that bring nutrients into the nearshore area and thus triggering phytoplankton blooms after the typhoon. Moreover, the positive apparent oxygen utilization (AOU) and unsaturated DO contents during the posttyphoon period suggest significant oxygen consumption (i.e., degradation process and biological respiration) caused by Typhoon Wipha in both nearshore and offshore areas. The internal nutrient recirculation and biological respiration are responsible for little change in POC, PN and nutrients in the offshore area between the pre‐ and posttyphoon periods and thus did not cause phytoplankton blooms. Our results suggest that the potential oxygen consumption (i.e., decomposition and biological respiration) after the typhoon are important biogeochemical impacts induced by Typhoon Wipha in coastal waters.