Abstract. A new data set of vertical column densities of the water vapour isotopologues H₂O and HDO from the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) instrument for the whole of the mission period from January 2003 to April 2012 is presented. The data are retrieved from reflectance measurements in the spectral range 2339 to 2383 nm with the Shortwave Infrared CO Retrieval (SICOR) algorithm, ignoring atmospheric light scattering in the measurement simulation. The retrievals are validated with ground-based Fourier transform infrared measurements obtained within the Multi-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water (MUSICA) project. A good agreement for low-altitude stations is found with an average bias of −3.6×10²¹ for H₂O and −1.0×10¹⁸ molec cm⁻² for HDO. The a posteriori computed δD shows an average bias of −8 ‰, even though polar stations have a larger negative bias. The latter is due to the large amount of sensor noise in SCIAMACHY in combination with low albedo and high solar zenith angles. To demonstrate the benefit of accounting for light scattering in the retrieval, the quality of the data product fitting effective cloud parameters simultaneously with trace gas columns is evaluated in a dedicated case study for measurements round high-altitude stations. Due to a large altitude difference between the satellite ground pixel and the mountain station, clear-sky scenes yield a large bias, resulting in a δD bias of 125 ‰. When selecting scenes with optically thick clouds within 1000 m above or below the station altitude, the bias in a posteriori δD is reduced from 125 to 44 ‰. The insights from the present study will also benefit the analysis of the data from the new Sentinel-5 Precursor mission.