Identifying and quantifying exchange flux across sediment-water interface is crucial when considering water and nutrient contributions to a eutrophic lake. In this study, observed temporal temperature distributions in shallow sediment of Lake Taihu (Eastern China) based on three-depth sensors at 14 sites throughout 2016 were used to assess temporal water exchange patterns. Results show that temporal temperature in shallow sediments differed with sampling sites and depths and the temperature amplitudes also clearly shrunk as the offshore distance increasing. Exchange fluxes estimated using the VFLUX 2 model based on temperature amplitude show that alternating-direction temporal flow exists in the eastern zone of Lake Taihu with averages of −13.0, −0.6, and 3.4 mm day−1 (negative represents discharging into the lake) at three nearshore sites (0.5, 2.0, and 6.0 km away from the shoreline, respectively). Whereas downwelling flow occurred throughout almost the entire year with averages of 37.7, 23.5, and 6.6 mm day−1 at the three southern nearshore sites, respectively. However, upwelling flow occurred throughout almost the entire year and varied widely in the western zone with averages of −74.8, 45.9, and −27.0 mm day–1 and in the northern zone with averages of −76.2, −55.3, and −51.1 mm day−1. The estimated fluxes in the central zone were relatively low and varied slightly during the entire year (−15.1 to 22.5 mm day−1 with an average of −0.7 mm day−1). Compared with the sub sensor pair (at 5 and 10 cm), the estimated hyporheic fluxes based on the top sensor pair (at 0 and 5 cm) varied within wider ranges and exhibited relatively larger values. Effects of upwelling flow at the western and northern zones need to be paid attention to on nearshore water quality particularly during winter and spring seasons. Estimated flow patterns at the four zones summarily reflect the seasonal water interaction near the sediment surface of Lake Taihu and are beneficial to improve its comprehensive management. Thermal dispersivity usually used for estimating the thermal diffusivity is more sensitive for upward hyporheic flux estimating even if with a low flux. Temperature amplitude ratio method can be used to estimate the exchange flux and suitable for low flux conditions (either upwelling or downwelling). A better evaluation of the exchange flux near inclined nearshore zones might need an optimized installation of temperature sensors along with the potential flow path and/or a vertical two-dimensional model in the future.