<p>The groundwater (GW) in the floodplain riparian area frequently interacts intensely with surface water (SW). Heat as a tracer is one of the hot research fields in investigating GW-SW interactions, and analytical approaches have been proposed for the calculation of exchange flow velocity. However, few studies have considered the effects of very dynamic flow conditions and monitoring instrumentation on the calculation with field measured data. Herein, taking the middle reaches of the Heihe River as the study area, different types of monitoring wells were constructed under the riverbed and near the river, and multiple methods (Darcy’s law, heat tracing, and isotopic mixing methods) were employed to trace the exchanges between the river and groundwater. The results indicate that different methods demonstrate diverse information with obvious unevenly distributed flux along the vertical direction. And the combination of multiple methods has an important role in studying the interaction between GW and SW. Fully screened wells produce intraborehole flow and disturb the heat transport, which is relevant to flow velocity, and further affects the temperature distribution, impacting the temperature-based flow velocity calculation. Dynamic flow conditions aggravate riverbed sediment disturbances, e.g., scour and deposition, and additionally affect the interaction and monitoring data.</p>