Water temperature is critical for growth and distribution of submerged macrophyte and heat flux at water-sediment interface (WSI) is essential for water temperature changes. East Lake Taihu is a typical shallow macrophyte-dominated lake in eastern China. Temperatures of water and sediment at different depths were monitored with high frequency from November 2013 to October 2015 in the middle of East Lake Taihu. Heat flux at WSI was calculated with inferred thermodynamic parameters. Changing patterns of water temperature and heat flux at WSI were revealed and their influencing factors were discussed. Results showed that the temperature rising processes were delayed with the increase of water depth. Water temperature rising process was prolonged in summer and shortened in winter. Temperature ranges in averaged 24 hours:surface water temperature > bottom water temperature > temperature at WSI > sediment temperature. Temperature ranges in averaged 24 hours were smallest in summer and largest in winter. There was a 1-days' hysteresis of temperature changes along the water depth when the temperature rose in spring and summer, while not in autumn and winter. Annual trends of temperatures in 2015 was same with 2014, and differences of year-on-year monthly averaged temperatures were significantly correlated with differences of air temperatures. Heat absorption of sediment from water increased or its heat emission to water decreased from 8:00 to 19:00, while 19:00 to 8:00 next day in verse. From March to September, heat transferred from water to sediment, while from sediment to water from October to February next year. Sediment was heat source of East Lake Taihu in a whole year. Heat flux at WSI also had smaller 6-15 days' periodic fluctuations. Although changes of water temperature and heat flux at WSI were mainly affected by solar radiation and air temperature, they had delayed response towards meteorological parameters. Heat flux at WSI was negatively correlated with water temperature, and its change lagged behind water temperature change. The main function of heat flux at WSI was to buffer heat changes of lake. Submerged plants can relief surface water temperatures of lake as well as the vertical temperature gradients in summer.