The fundamental exchange of water for carbon lays the groundwork for understanding the interplay between carbon and water cycles in terrestrial ecosystems, providing valuable insights into global water and carbon balances and vegetation growth. Inherent water use efficiency (IWUE) was used as a study framework of the diurnal patterns and degree of coupling of carbon and water exchange to investigate the net ecosystem carbon exchange (NEE) responses of three water regime potato cropping systems [full-irrigation (FI), deficit-irrigation (DI), and rainfed (RF)] in Cundinamarca, Colombia. The eddy covariance method was used to determine CO2 and water fluxes, surface resistances, and the omega decoupling factor (Ω). Additionally, leaf area index (LAI), and specific leaf area (SLA) were assessed to determine the canopy influence on carbon and water exchange. The highest carbon sink activity (NEE = -311.96 ± 12.82 g C m−2) at FI, is primarily attributed to a larger canopy with high autotrophic activity and low internal resistance. This supported a highly coupled and synchronized exchange between evapotranspiration (ET) and gross primary production (GPP), as reflected in the highest IWUE (4.7 mg C kPa s−1 kg−1 H2O). In contrast, the lower sink capacity at DI (NEE = − 17.3 ± 4.6 g C m−2) and the net carbon source activity from RF (NEE = 187.21 ± 3.84 g C m−2) were related to a smaller leaf area available for water and carbon exchange, resulting in lower IWUE (2.3 and 1.01 mg C kPa s−1 kg−1 H2O, respectively) and a decoupled and desynchronized gas exchange caused by unbalanced restrictions on ET and GPP fluxes. These results provide new information on carbon–water interactions in potatoes and improve the understanding of carbon sequestration and drought effects on potato sink activity.