Gross α and β indices for water samples are generally determined simultaneously when a gas-flow proportional counter is used. The thickness of the source and the α-particle energy are factors of great importance due to self-absorption or energy loss effects. Two variables have been studied: the use of different salts to produce standards with several thicknesses and the use of different radionuclides for the calibration process. Samples of known activity were prepared and measured for checking the procedures. •Gross alpha and beta indices are measured with a gas-flow proportional counter.•Sample thickness is important due to self-absorption or energy loss effects.•Sodium carbonate, nitrate and sulphate were used for the attenuation curves.•226Ra, Natural uranium, 241Am, 209Po, and 242Pu were used for calibration.