The Itoigawa-Shizuoka tectonic line formed the largest inland tectonic basin in Japan. Taking advantage of the characteristics of the large tectonic basin, this study aims to clarify the hydrological response related to groundwater recharge and discharge in this area from field measurements such as monthly spring discharge measurements in the spring belt, infiltration measurements of irrigation recharge in rice paddy fields and analysis of stable isotopic ratios of oxygen and hydrogen. Volumetric water flow measurements in the tectonic basin demonstrate that the hydrological response function (HRF) is expressed as a linear equation. Despite the complex topography and geology of the mountain catchment and artificial recharge within the basin, this HRF is maintained, except for forced artificial irrigation in August when the natural water supply is significantly reduced, and except in March and April when snowmelt flows into the river. This study clarifies that monthly fluctuations in total groundwater flow within a basin can be estimated by applying HRF to monitoring data of total surface flow at the farthest downstream. The field measurements demonstrate that the rainfall in the mountain catchment area and artificial irrigation recharge in the basin greatly influence the fluctuation of groundwater flow rate, especially on the fluctuation of the spring water in the spring belt. Field data inferred that the frequent depletion of the springs in the inland tectonic basin, where all groundwater emerges at the most downstream, depends on the rapid decline in annual rainfall in mountain catchment areas. These observations suggest that the total groundwater resource in this region was affected not only by reduced irrigation recharge due to the historical paddy acreage reduction program implemented in Japan from 1971 to 2018, and by excessive groundwater extraction, but also by rapid decline in annual rainfall in mountain catchments that occurs non-periodically.