The data consist of stable water isotope composition in the rivers , lakes, soils and flooded areas in the Western Siberia Lowlands (WSL). Sampling area encompassed a 1700 km south-north transect spanning from approx. 56°N to 68°N in latitude and 74°E to 84°E in longitude. Samples were collected during multiple field campaigns between February 2014 and November 2016. The dataset in produced as a part of the JPI/NERC funded SIWA project 'Climate impact on the carbon emission and export from Siberian inland waters'. The dataset has resulted in two publications submitted to peer-review: (i) Ala-aho et al. (2018). Using stable isotopes to assess surface water source dynamics and hydrological connectivity in a high-latitude wetland and permafrost influenced landscape. Journal of Hydrology, 556, 279-293. (ii) Ala-aho et al. (2018). Permafrost and lakes control river isotope composition across a boreal Arctic transect in the Western Siberian lowlands. Environmental Research Letters, 13(3), 34028.