Groundwater is one of the key sources of water recharge in Hulun Lake. In order to trace the location of the confined aquifer of the deep groundwater that recharges the lake, hydrogeochemical characteristic analysis and hydrogen and oxygen stable isotope sampling and analysis were performed on the lake water, phreatic water and multi-layer cretaceous confined water in the same region of the Hulun Lake basin. The hydraulic relationships between the lake and various aquifers were then revealed through the use of hydrogen radioisotopes. The results show that the lake water, phreatic water and confined water are of the HCO3−Na type, and the content of stable isotopes (δD, δ18O) and radioisotopes (δ3H) is in the order of “confined water < phreatic water < lake water”. The main influencing factor of hydrochemical evolution in the phreatic water is the dissolution of feldspar; its age is about 26.66 years, and its renewal rate is nearly 3.75%. The main influencing factor of hydrochemical evolution in the K1y1, K1y2 and K1d1 Cretaceous confined water is evaporite dissolution (i.e., halite, gypsum); their renewal rate is less than 1%, and the discharge condition deteriorates with the increase in the aquifer roof burial depth. Phreatic water in the Jalainur Depression Zone supplies Hulun Lake under the condition of the existence of permafrost cover. The K1d2 confined water of the Lower Cretaceous–Damoguaihe Formation Coal Group II, with the deepest roof burial depth (441 m), shows significant differences in hydrochemistry, δD, δ18O and δ3H from the other K1y1, K1y2 and K1d1 Cretaceous confined waters in the same basin. The renewal rate (nearly 4.32%) of the K1d2 confined water is better than that of the phreatic water, and its hydrochemical characteristics are similar to those of the lake water and phreatic water, indicating that the Cuogang Fault and Xishan Fault, caused by crustal faults, resulted in the hydraulic relationship between the K1d2 confined water, lake water and phreatic water, resulting in drastic interannual changes in the lake water level. This study of lake–groundwater interactions in cold and arid regions can provide a theoretical basis for lakes’ sustainable development.