Abstract The present work deals with determination groundwater flows in the Amazon region, based on analysis of geothermal data acquired in shallow and deep wells. The method employed is based on the model of simultaneous heat transfer by conduction and advection in permeable media. Analysis of temperature data acquired in water wells indicates down flows of groundwaters with velocities in excess of 10−7m/s at depths less than 300m in the Amazonas basin. Bottom-hole temperature (BHT) data sets have been used in determining characteristics of fluid movements at larger depths in the basins of Acre, Solimões, Amazonas, Marajó and Barreirinhas. The results of model simulations point to down flow of groundwaters with velocities of the order of 10−8 to 10−9m/s, at depths of up to 4000m. No evidence has been found for up flow typical of discharge zones. The general conclusion compatible with such results is that large-scale groundwater recharge systems operate at both shallow and deep levels in all sedimentary basins of the Amazon region. However, the basement rock formations of the Amazon region are relatively impermeable and hence extensive down flow systems through the sedimentary strata are possible only in the presence of generalized lateral movement of groundwater in the basal parts of the sedimentary basins. The direction of this lateral flow, inferred from the basement topography and geological characteristics of the region, is from west to east, following roughly the course of surface drainage system of the Amazon River, with eventual discharge into the Atlantic Ocean. The estimated flow rate at the continental margin is 3287m3/s, with velocities of the order of 218m/year. It is possible that dynamic changes in the fluvial systems in the western parts of South American continent have been responsible for triggering alterations in the groundwater recharge systems and deep seated lateral flows in the Amazon region.