The study of the dynamics of anthropic disturbances that have an effect on the hydrological systems in plains requires integral simulation tools for their diagnosis. The objective of this article is, first, to analyse and reproduce the spatio‐temporal interactions between groundwater (GW) and surface water, net recharge, GW level, surface run‐off, and evapotranspiration in the upper creek basin of Del Azul, which is located in the centre of the province of Buenos Aires, Argentina, and second, to obtain insights to apply the methodology to other similar situations. For this purpose, a model coupling the semidistributed hydrological model (Soil and Water Assessment Tool [SWAT]) and the hydrogeological model (MODFLOW) has been used. A simulation was carried out for a period of 13 years (2003–2015) on a daily scale. The application of the SWAT–MODFLOW coupling gave good results based on the adjustment between the calculated flows and levels, reaching a Nash–Sutcliffe of 0.6 and R20.6 at the Seminario hydrometric station located at the watershed outlet point. According to the annual average balance, out of the total rainfall, evapotranspiration accounts for 85%, recharge accounts for 10.2%, and surface run‐off accounts for 4.8%. Annual and monthly trends of the stream–aquifer interaction were determined, obtaining on average an annual GW discharge of 34 mm and an annual average recharge of the stream to the aquifer of 1.4 mm. Monthly GW discharges are higher in winter–spring (July to December with an average of 3.3 mm) and lower in summer–autumn (January to June with an average of 2.8 mm). The monthly average recharge of the stream towards the aquifer varies from 0.02 to 0.36 mm and is higher in March, May, and August, when water excess is produced in the basin. Through the analysis of coupled modelling, it is possible to analyse and reproduce the spatio‐temporal transitions of flow existing between the stream, the hyporheic zone, and the aquifer.