Methane (CH4) fluxes were measured in hypereutrophic Meiliang Bay of Taihu Lake with static chambers for 1 year. The results showed that the macrophyte-covered infralittoral zones were the “hotspots” of CH4 emission in water systems. There were large temporal variations for CH4 fluxes, ranging from −1.7 to 131 mg CH4 m−2 h−1, in the macrophyte-covered littoral zone. The highest CH4 emissions occurred during the period of the summer algal bloom. The amount of CH4 flux from June to September accounted for about 50–90% of the annual fluxes. CH4 fluxes from the bare infralittoral zone (−0.2∼4.2 mg CH4 m−2 h−1) were low and close to those in the pelagic zone. The difference in CH4 fluxes between macrophyte-covered and bare infralittoral zones indicated that vegetation in the inundated area played an essential role in CH4 production. In the infralittoral zone, the redox condition (DO, Eh), temperature, and primary production controlled CH4 fluxes; these variables explained 47% of flux variation, whereas such influences were not detected in the pelagic zone.