For many of the Siberian rivers, and the Upper Ob in particular, 70–80% of the volume of the annual water runoff is formed during the spring flood. Thus, factors influencing the formation of water runoff during the spring flood are paramount. We explain changes in the isotopic composition of the Upper Ob surface waters by changing different components’ contribution to the runoff water discharge over the spring flood period. We suggest estimating the time of meltwater flow from the Upper Ob watershed to the outlet section using the difference between the date of the complete melting of the snow cover in the catchment area and the date of the maximum light isotope composition of water in the outlet section. We show that a sharp short-term weighting of the isotopic composition of water in the river at the end of the first phase of the flood may be associated with the influx of autumn soil moisture, displaced from the soils by snowmelt waters.