Groundwater in the Benegov-Usti aquifer system in the northwestern Bohemian Cretaceous basin has been intensely exploited since the twentieth century. Apart from providing drinking water, it contains the most extensive accumulation of thermal water in the country. However, excessive exploitation can result in temperature declines and changes in the quality of the groundwater in the future. More than a hundred in situ temperature measurements were used to assess the geothermal gradient and heat flux. However, intense groundwater vertical-flow across the well significantly controls the heat flux distribution, resulting in a huge range of values from less than 50 mW/m(2) within infiltration areas to more than 125 mW/m(2) in drainage areas. Certain simplifications and corrections considering the vertical flow between different permeable zones were developed, and the correction for topography as well as lithological variability have been applied to improve accuracy of the geothermal gradient assessment. Despite the fact that the Bohemian Cretaceous basin is tectonically very complex, it is concluded that tectonics [with the exception of the Eger (Ohre) rift] has only a secondary effect on the thermal field. Two longitudinal W-E areas in the Benesov-Usti aquifer system have elevated heat flux values. The calculated heat flux values are useful for heat transfer modelling and the assessment of the sustainable limits of thermal water exploitation. (C) 2011 Elsevier Ltd. All rights reserved.