Freshwater supplementation is often used for wetland restoration and ecosystem health protection. Understanding temporal patterns of aquatic metabolism caused by freshwater supplementation may help optimize wetland restoration designs. We investigated the short-term changes in aquatic metabolism and potential driving factors at two sites dominated by Phragmites australis and Suaeda salsa, respectively, in a restored coastal wetland located in the Yellow River Delta. Results showed that metabolism was influenced by freshwater supplementation. There was a wide range of variation in gross primary production (GPP) from 0.04 to 49.78 mg O2 L−1 d−1, ecosystem respiration (ER) from 3.37 to 45.86 mg O2 L−1 d−1, and net ecosystem metabolism (NEM) from −12.92 to 9.01 mg O2 L−1 d−1. GPP was more sensitive than ER as a response to flooding and, thus, decreases in NEM led to change of ecosystem from autotrophic to heterotrophic or from heterotrophic to more heterotrophic within one day. Several factors, including water depth, nutrient, salinity, pH, and turbidity, collectively influenced the variation in metabolism. Salinity is a particularly important factor that affected the metabolism rate of the coastal wetland. These findings suggest that a moderate water flow rate (e. g., ≤ 20 cm d−1) may help increase GPP post-flooding.