Comprehending the hydrological conditions in wetlands is a critical aspect of successfully enhancing wetland conservation. The interaction between wetland surface water and groundwater is a complex process, requiring detailed onsite hydrological and soil surveys, laboratory experiments, and modeling to clarify this relationship. However, conventional investigation methods often cause significant disruptions and thus may affect the natural environment and compromise data reliability. In this study, a high-accuracy and low-environmental-disturbance (LED) approach was proposed involving modified falling head permeability and modified seepage meter tests to elucidate the groundwater characteristics in an ecological reserve. A water balance (WB) calculation method was employed to examine the performance of the proposed LED approach. The results revealed that the LED performed better than conventional methods in hydraulic conductivity and seepage velocity exploration, thereby improving the accuracy of quantifying groundwater flow. Moreover, the experimental findings and ecohydrological observations were used to assess the groundwater flow regime, and the data were consistent with the field survey results. The contradiction between conducting research and protecting ecological reserves can pose difficulties in the sustainable and effective management of wetlands. The LED approach can be applied broadly, especially in areas where significant disturbance should be avoided. The water budget model can thus be developed to help deduce the interaction between groundwater and surface water. We suggest that these innovative methods are effective tools and can assist both scientists and authorities in formulating corresponding habitat management strategies.