Better understanding of surface water (SW) and groundwater (GW) interactions and water balances has become indispensable for water management decisions. This study sought to characterize SW-GW interactions in three crop fields located in three different irrigated valleys in northern New Mexico by (1) estimating deep percolation (DP) below the root zone in flood-irrigated crop fields; and (2) characterizing shallow aquifer response to inputs from DP associated with irrigation. Detailed measurements of irrigation water application, soil water content fluctuations, crop field runoff, and weather data were used in the water budget calculations for each field. Shallow wells were used to monitor groundwater level response to DP inputs. The amount of DP was positively and significantly related to the total amount of irrigation water applied for the Rio Hondo and Alcalde sites, but not for the El Rito site. The average irrigation event DP using data for the complete irrigation season at each of the three sites was 77.0 mm at El Rito, 54.5 mm at Alcalde and 53.1 mm at Rio Hondo. Groundwater level rise compared to pre-irrigation event water levels ranged from 3 to 1870 mm, and was influenced by differences in irrigation practices between sites. Crop evapotranspiration estimates averaged across irrigation events were highest in Rio Hondo (22.9 mm), followed by El Rito (14.4 mm) and Alcalde (10.4 mm). Results from this study indicate there are strong surface water-groundwater connections in traditionally irrigated systems of northern New Mexico, connections that may be employed to better manage groundwater recharge and river flow.