Conceptual rainfall-runoff models besides precipitation and discharge data generally require estimates of the mean daily air temperature as input data. For the estimation of the mean daily air temperature, there are different methods available. The paper presents an evaluation of the impact of the mean daily air temperature calculation on the rainfall-runoff modelling results. Additionally, other measured variables and rating curve uncertainty were assessed. Differences in the mean daily air temperature values were evaluated for the 33 meteorological stations in Slovenia and additional investigations were conducted for four selected meso-scale catchments located in different climates. The results of the application of four equations for the mean air temperature calculation yielded the mean absolute error values between 0.56–0.80 °C. However, the results of rainfall-runoff modelling showed that these differences had an almost negligible impact on the model results. Differences in the mean simulated discharge values were no larger than 1%, while differences in the maximum discharge values were a bit larger, but did not exceed 5%. A somewhat larger impact on the model results was observed when precipitation and water level measurements’ uncertainty was included. However, among all analysed input data uncertainties, the rating curve uncertainty can be regarded as the most influential with differences in the simulated mean discharge values in the range of 3% and differences in the maximum discharge values up to 14%.