The expansion of rainfed agriculture, especially soybean cultivation in sub-humid plains, alters water balance and the exchange between groundwater-surface water (GW-SW). However, to date, there are no studies that analyze how these anthropic disturbances affect hydrological connectivity in these systems, especially the GW-SW interactions. The objective of this study is to analyze how the increase in rainfed agriculture affects the spatio-temporal patterns of the water balance and the GW-SW interaction. For this analysis, a coupled GW-SW flow model was implemented under land use and land cover (LULC) scenarios, to quantify the spatio-temporal dynamics for different components of water balance and GW-SW interactions for the upper creek basin of Del Azul. A simulation was carried out for a period of 13 years (2003–2015) on a daily scale and it was contrasted through three multitemporal LULC maps. The results point that substitution of natural pastures, the reduction of winter crops and the decrease of crop rotation, due to the increase of soybean monoculture in the basin under study, modifies the water balance, especially the annual rates of surface runoff and soil moisture which may increase between 3.5 and 9.4 % and between 1.4 and 4.4 % respectively, thus increasing the annual streamflows between 2.6 and 6.8 % and the groundwater heads between 0.2 and 0.6 m. This leads to changes in the hetereogeneity of the GW-SW interaction, a reduction between 0.3 and 3 % is observed in the discharge from the Pampeano aquifer to the Del Azul stream, while the recharge rates from the Del Azul stream to the Pampeano aquifer increase between 2 and 17.8 %. The application of the SWAT-MODFLOW model under LULC scenarios, improves the prediction of the regional hydrologic connectivity on sub-humid plains, because the hydrological processes occurring in the surface and non-saturated zone are governed by shallow groundwater dynamics.