Groundwater and surface water form an integrated system that is essential to understanding and managing mountain water resources. Mountain hydrology is inherently complex due to steep elevation gradients, diverse climates, complex geology, the presence or absence of cryosphere elements, and rapid climate change. Groundwater plays a crucial role in the mountain hydrologic systems, yet key questions persist, including: how much water enters each subsystem? How can we quantify this partitioning? And how do climate change, cryosphere loss, and human activities affect groundwater function for water resources? We present research on long-term groundwater trends in mountain regions using data from observation wells across Canada and the United States, each with at least 20 years of monthly records. We find that more than two-thirds of the observation wells show declines in groundwater storage, with stronger positive and negative trends occurring in the western mountain ranges. Statistical analyses finds that groundwater fluctuations are influenced by geology and that declines are most pronounced in lower-elevation regions with higher temperatures and lower precipitation. Our research highlights that climate change-driven shifts in mountain hydrology extend to the subsurface, with critical implications for global water resources.