Novel low-pressure irrigation technologies have been widely adopted by farmers, allowing both reduced water and energy use. However, little is known about how the transition from legacy technologies affected water and energy use at the aquifer scale. Here, we examine the widespread adoption of low-energy precision application (LEPA) and related technologies across the Kansas High Plains Aquifer. We combine direct energy consumption and carbon emission estimates with life cycle assessment to calculate the energy and greenhouse gas (GHG) footprints of irrigation. We integrate detailed water use, irrigation type, and pump energy source data with aquifer water level and groundwater chemistry information to produce annual estimates of energy use and carbon emissions from 1994 to 2016. The rapid adoption of LEPA technologies did not slow pumping, but it reduced energy use by 19.2% and GHG emissions by 15.2%. Nevertheless, water level declines have offset energy efficiency gains because of LEPA adoption. Deeper water tables quadrupled the proportion of GHG emissions resulting from direct carbon emissions, offsetting the decarbonization of the regional electrical grid. We show that low-pressure irrigation technology adoption, absent policies that incentivize or mandate reduced water use, ultimately increases the energy and carbon footprints of irrigated agriculture.