Abstract: Although the hydrological state of the lower Yangtze River’s tidal portion is quite complex, its effects on the dynamics of the wetland water, heat, and salt are not well understood. This study used the Lvshuiwan wetland in the Nanjing section of the Yangtze River as its research subject. We tracked the wetland’s hydrological changes and their signal characteristics, built a model of the wetland’s hydrothermal transport and nitrogen migration and transformation, and discussed how tidal processes affected the wetland’s hydrothermal storage and nitrogen removal as well as its seasonal variations. The findings indicated that runoff and tide, with significant runoff in spring and summer and increased tidal fluctuation in autumn and winter, are two signal characteristics that contribute to changes in water level and temperature in the wetland. The amount of nitrogen removed from the wetland due to runoff is three to five times more during spring and summer due to the rise in river water level, temperature, and dissolved oxygen at the water-soil interface. Nevertheless, the amplitudes of tidal fluctuations in autumn and winter are roughly twice as large as those in spring and summer, which significantly improves the nitrogen removal of the wetland and increases the nitrogen removal efficiency by about 63% and 31% on the basis of that driven by runoff, making it about 2.5–5 times as large as in spring and summer. The findings of the study offer a theoretical framework for the ecological protection of the tidal river wetland in the lower Yangtze River.