Relevance. The need for a more accurate assessment of the underground component of river runoff as a basis for assessing groundwater resources and solving a number of hydroecological problems. Aim. To develop a methodology and actually assess the underground component of the Ob river runoff in its middle reaches using hydrogeological and hydrological data. Methods. Mathematical modeling, statistical methods. Results and conclusions. Based on the analysis of hydrogeological and hydrological materials for a conditionally homogeneous period of 1995–2015, a methodology has been developed for assessing the underground component of river runoff within the West Siberian Plain using data on average monthly discharges and river water levels in winter low water and groundwater levels (in the zone of active water exchange). The methodology is maximally adapted to the requirements of the current Russian legislation and includes an analysis of the hydrogeochemical balance and the determination of parameters that correspond to the filtration coefficient and specific groundwater inflow using mathematical statistics and optimization methods. The method was tested on the example of the Ob and large tributaries in its middle reaches. It was established that in most cases medium and large rivers are characterized by the prevalence of a descending mode of interaction between river and groundwater in general within river valleys, and the lower limit of determining the underground component of river runoff can be determined using linear interpolation between the flows in March and December. It was shown that hydrogeological conditions previously (in the Upper Cretaceous and Paleogene) could have contributed (and currently contribute) to the accumulation of iron compounds in the upper hydrogeodynamic zone.