Long-term atmospheric CO₂ mole fraction and δ¹³CO₂ observations over North America document persistent responses to the El Niño-Southern Oscillation. We estimate these responses corresponded to 0.61 (0.45 to 0.79) PgC year^-1 more North American carbon uptake during El Niño than during La Niña between 2007 and 2015, partially offsetting increases of net tropical biosphere-to-atmosphere carbon flux around El Niño. Anomalies in derived North American net ecosystem exchange (NEE) display strong but opposite correlations with surface air temperature between seasons, while their correlation with water availability was more constant throughout the year, such that water availability is the dominant control on annual NEE variability over North America. These results suggest that increased water availability and favorable temperature conditions (warmer spring and cooler summer) caused enhanced carbon uptake over North America near and during El Niño.