This paper investigates the approaches to the formation of balance movement patterns of financial flows in the regional territorial system, analyzes the main advantages and disadvantages. Special attention is paid to the analysis of the possibilities of using the System of National Accounts for the formation of a matrix of financial flows between institutional sectors at the regional level. The paper presents a theoretical and methodological approach to the formation of the matrix of financial flows between institutional sectors on the basis of ordering and processing of primary accounting data that reflect the interaction of credit institutions, insurance companies, pension funds, asset management industry from other institutional sectors. Formation of the matrix of financial flows, in accordance with the proposed approach, carried out using the principle of double-entry, according to which the changes taking place on the financial assets of the institutional sector, leads to a proportional change in the liabilities of other sectors in the framework of the instrument for which there is a movement of financial flows. The proposed approach has been implemented by the author during the formation of the matrix of financial flows in the Sverdlovsk region in 2014, which allowed to reflect legitimate processes of financial flows between institutional sectors, identify trends, emerging risks in the financial sector development in the region. Developed in the course of a matrix approach presented in the future will be a means for forecasting and scenario modeling of the distribution of financial resources among the institutional sectors in the future.