In the case of absence of reliable information on fluctuations of levels and hydraulic parameters of aquifers within a large catchment, the method of river hydrograph decomposition can be used to assess groundwater component and other constituents of river water recharge. The difficulties and shortcomings of this method, which relies on specific schematizations and assumptions, are analysed and discussed. We propose to take into account the results of calculations of lateral groundwater inflow to the river accomplished using the numerical method based on observations at representative balance sites in order to improve the accuracy of the method of decomposition of the river hydrograph. A proper schematization should also be justified for river catchment (or its part), which describes the interaction of surface water, shallow groundwater, and artesian (deep) interlayer waters, which provides rationale for defining or neglecting groundwater inflow to river during the flood periods. The most disputable issue remains the allocation of the phase of “reverse water inflow to river banks” during flood periods. The groundwater level rise at the beginning of the flood results from the infiltration recharge to the aquifer and from inflow of water from the river. The contribution of inflow to river bank to groundwater level rise is dependent from the distance from the river to the observation well. To establish hydraulic head gradient from the river towards the adjacent groundwater aquifer at flood peak, at least two observation wells are needed, one of which should be located 3–4 m from the river water edge on the elevated part of the bank which is not flooded, and the other should be located 50–70 m from the bank towards the watershed. It is proposed that the phase of maximum groundwater inflow to the river should be adjusted based on the dates of the beginning and ending of the groundwater level decrease during the recession of the river flow during the flood period. The combined application of the described above methods showed that the use of only hydrograph decomposition method underestimates the share of groundwater recharge to the river by 2–5%. Based on the analysis of the Pivdennyi Buh River hydrographs during the 1980–2020 period, general tendencies of changes in the shallow groundwater and deep subsurface recharge of the Pivdennyi Buh River in its upper basin (upstream of the city of Khmilnyk) have been established: deep subsurface recharge prevailed over the shallow groundwater component (33.4 compared to 25.0% of the total). At the same time, the total subsurface runoff constituted on average 58%.