Some of the world’s key agricultural production systems face big challenges to both water quantity and quality due to shallow groundwater that results from long-term intensive irrigation, namely waterlogging and salinity, water losses, and environmental problems. This paper focuses on water quantity issues, presenting finite-difference groundwater models developed to describe shallow water table levels, non-beneficial groundwater consumptive use, and return flows to streams across two regions within an irrigated alluvial river valley in southeastern Colorado, USA. The models are calibrated and applied to simulate current baseline conditions in the alluvial aquifer system and to examine actions for potentially improving these conditions. The models provide a detailed description of regional-scale subsurface unsaturated and saturated flow processes, thereby enabling detailed spatiotemporal description of groundwater levels, recharge to infiltration ratios, partitioning of ET originating from the unsaturated and saturated zones, and groundwater flows, among other variables. Hybrid automated and manual calibration of the models is achieved using extensive observations of groundwater hydraulic head, groundwater return flow to streams, aquifer stratigraphy, canal seepage, total evapotranspiration, the portion of evapotranspiration supplied by upflux from the shallow water table, and irrigation flows. Baseline results from the two regional-scale models are compared to model predictions under variations of four alternative management schemes: (1) reduced seepage from earthen canals, (2) reduced irrigation applications, (3) rotational lease fallowing (irrigation water leased to municipalities, resulting in temporary dry-up of fields), and (4) combinations of these. The potential for increasing the average water table depth by up to 1.1 and 0.7 m in the two respective modeled regions, thereby reducing the threat of waterlogging and lowering non-beneficial consumptive use from adjacent fallow and naturally-vegetated lands, is demonstrated for the alternative management intervention scenarios considered. Net annual average savings of up to about 9.9 million m³ (8000 ac ft) and 2.3 million m³ (1900 ac ft) of non-beneficial groundwater consumptive use is demonstrated for the study periods in each of the two respective study regions. Alternative water management interventions achieve varying degrees of benefits in each of the two regions, suggesting a need to adopt region-specific interventions and avoid a ‘one-size-fits-all’ approach. Impacts of the considered interventions on return flows to the river were predicted to be significant, highlighting the need for flow augmentation to comply with an interstate river compact and portending beneficial impacts on solute loading.