Potato farming is relevant for global carbon balances and greenhouse emissions, of which gross primary productivity (GPP) is one of the main drivers. In this study, the net carbon ecosystem exchange (NEE) was measured using the Eddy Covariance (EC) method in two potato crops, one of them with an irrigation system, the other under rainfed conditions. Accurate NEE partition into GPP and ecosystem respiration (RECO) was carried out by fitting a light response curve. Direct measurements of dry weight and leaf area were performed from sowing to the end of canopy life cycle and tuber bulking. Agricultural drought in the rainfed crop resulted in limited GPP rate, low leaf area index (LAI), and low canopy carbon assimilation response to the photosynthetically active radiation (PAR). Hence, in this crop, there was lower efficiency in tuber biomass gain and NEE sum indicated net carbon emissions to atmosphere (NEE = 154.7 g C m−2 ± 30.21). In contrast, the irrigated crop showed higher GPP rate and acted as a carbon sink (NEE = −366.6 g C m−2 ± 50.30). Our results show, the environmental and productive benefits of potato crops grown under optimal water supply.