Most of the world's permafrost is located in the Arctic, where its frozen organic carbon content makes it a potentially important influence on the global climate system. The Arctic climate appears to be changing more rapidly than the lower latitudes, but observational data density in the region is low. Permafrost thaw and carbon release into the atmosphere, as well as snow cover changes, are positive feedback mechanisms that have the potential for climate warming. It is therefore particularly important to understand the links between the energy balance, which can vary rapidly over hourly to annual timescales, and permafrost conditions, which changes slowly on decadal to centennial timescales. This requires long-term observational data such as that available from the Samoylov research site in northern Siberia, where meteorological parameters, energy balance, and subsurface observations have been recorded since 1998. This paper presents the temporal data set produced between 2002 and 2017, explaining the instrumentation, calibration, processing, and data quality control. Furthermore, we present a merged data set of the parameters, which were measured from 1998 onwards. Additional data include a high-resolution digital terrain model (DTM) obtained from terrestrial lidar laser scanning. Since the data provide observations of temporally variable parameters that influence energy fluxes between permafrost, active-layer soils, and the atmosphere (such as snow depth and soil moisture content), they are suitable for calibrating and quantifying the dynamics of permafrost as a component in earth system models. The data also include soil properties beneath different microtopographic features (a polygon centre, a rim, a slope, and a trough), yielding much-needed information on landscape heterogeneity for use in land surface modelling. For the record from 1998 to 2017, the average mean annual air temperature was −12.3 ∘C, with mean monthly temperature of the warmest month (July) recorded as 9.5 ∘C and for the coldest month (February) −32.7 ∘C. The average annual rainfall was 169 mm. The depth of zero annual amplitude is at 20.75 m. At this depth, the temperature has increased from −9.1 ∘C in 2006 to −7.7 ∘C in 2017. The presented data are freely available through the PANGAEA (https://doi.org/10.1594/PANGAEA.891142) and Zenodo (https://zenodo.org/record/2223709, last access: 6 February 2019) websites.