CH4 emissions have been widely studied in various wetlands, such as boreal peatlands, rice paddies, and tropical swamps. However, little investigation has been carried out for CH4 emissions from lakes or wetlands in arid regions where these freshwaters play a vital role in providing ecosystem services for local people. To quantify the spatial and temporal variations of CH4 flux and understand its key controlling factors in shallow lakes in arid regions of Western China, CH4 fluxes from Wuliangsu Lake were measured at different vegetation zones and water depths with a static chamber technique during a growing season from April to October in 2003. Results showed that the average emission flux of CH4 from submerged plant (Potamogeton pectinatus) growing zones was 2.16mg CH4 m−2 h−1, which was 85.8% lower than that from emergent macrophyte (Phragmites australis) growing zones. CH4 emissions increased with increasing water depth in Phragmites Community. Significant seasonal and diurnal variations of CH4 emission were observed for P. australis during the plant growth stage, for P. pectinatus growing zones, however, the variations were minor. In addition to vegetation cover and water depth, bottom silt temperature and light intensity were also important factors influencing seasonal and diurnal variations of CH4 flux from Phargmites growing zone.