Beavers (Castor canadensis) alter river corridor hydrology by creating ponds and inundating floodplains, and thereby improving surface water storage. However, the impact of inundation on groundwater, particularly in mountainous alluvial floodplains with permeable gravel/cobble layers overlain by a soil layer, remains uncertain. Numerical modeling across various floodplain structures considers topographic and sediment complexity and multidirectional flow, linking inundation to groundwater response. This study develops a model-data integration workflow to address uncertainty in groundwater response to beaver-induced inundations in a mountainous alluvial floodplain in the Upper Colorado River Basin. Uncertain factors include seasonal hydrologic dynamics, hydraulic conductivities, floodplain structures, and meteorological forcings. We employed an ensemble of groundwater models, based on geophysical and hydrologic data, with machine learning-based calibration using a neural density estimator. This allowed us to quantify the vertical flux from the soil layer to the permeable gravel bed, the down-valley underflow within the gravel bed, and their ratios. Results show a significant increase in the vertical flux relative to down-valley underflow, from 2% during dry pond periods to 20% during wet periods, serving as an analogy for conditions without and with beaver ponds. The study highlights the influence of floodplain structure on groundwater storage, water balance, and water quality impacted by beaver ponds. A thick gravel bed layer, with a large down-valley underflow, minimizes the effect of beaver-induced inundation on water quality. We emphasize the need for field-scale measurements of floodplain structure and improved characterization of evapotranspiration changes to reduce uncertainty in groundwater response.