Water in the western United States is a stressed commodity due to high climate variability, growing water demands, and difficulties capturing and storing water during extreme precipitation events that also pose flooding hazards. In California, atmospheric rivers (ARs) contribute up to half of annual precipitation and compose many of the largest storms. Their magnitude and frequency of occurrence are also expected to increase in the future due to climate change. However, the impact of these ARs on the integrated hydrologic cycle, and specifically the role of ARs on groundwater hydrodynamics, is largely unknown. Travel pathways and water residence times of AR water through a watershed are difficult to trace and quantify in situ, which complicates water resource decision making. For example, uncertainty still exists in the hydrologic connection between storms in the Sierra Nevada mountains (where the majority of California’s precipitation falls) and flow in the Central Valley (where the water is used for agriculture or further transported to metropolitan regions). To better understand the behavior of AR versus non-AR event water, we pair the high-resolution (500 m) regional climate model WRF to the coupled land surface-groundwater model ParFlow-CLM, which solves the water energy balance in three dimensions. High performance computing is used to simulate subsurface flow and interaction with the atmosphere at scales ranging from 10 cm at the land surface to tens of meters into subsurface aquifers. The integrated hydrologic model is then coupled to a new ecohydrologic Lagrangian particle tracking code, EcoSLIM, which traces water parcels through their complete lifecycle in a watershed, including: deposition, infiltration, surface and subsurface transport, and return to the atmosphere via evapotranspiration. The TempestExtremes AR detection algorithm is used to determine periods of ARs, and groups them into categories based on their potential benefit or hazard. This novel method to quantify AR contributions to the hydrologic cycle and to track flow pathways throughout the watershed can be used to inform water resilience strategies such as managed aquifer recharge (MAR) and flood-hazard mitigation, especially for a future where AR precipitation events may account for an even larger portion of the water year totals.