The article aims to examine the peculiarities of the financial mechanism of the transboundary natural resources management, which is very diversified all over the world and comprises: trust funds, ongoing revolving funds, public-private partnerships, public funding in member countries. Promoting the transboundary cooperation of natural resources management is characterized with frequent underfunding and resolving its mechanisms is not sufficient. The lack of transboundary management funding is reflected by weak results of institutional development of the transboundary regions in their entirity. The process of funding of the transboundary natural resources management should consist of four major steps to promote the development of the transboundary institutional mechanisms: the initiation process, institutional mechanism, program realization and investments within the common management of the transboundary natural resources. The article defines the following principles of the financial mechanism for transboundary natural resources management: the principle of the annual contribution of each member country to the Euroregion budget, the polluter-pays principle, the principle of fund receiving for the provision of services. On the grounds of the analysis of foreign experiences we offer two ways of creating specific funds to support the transboundary water resources management, such as: special financing fund and basin trust fund. The effective managing of the transboundary natural resources demands the presence of the local goverment institutions which may aid the cooperation between countries and realization of the common strategy and managing policy. The proper funding of the transboundary cooperation mechanisms and transboundary institutions, which manage these resources, should be performed steadily. Especially funding the creation and maintainance of the institutional mechanisms, building a potential, developing legal frameworks, managing (including monitoring of the data exchange and evaluation), and supporting the realization of common programs of optimalization of fair use of and protection of common transboundary natural resources. All the traditional and innovative financial mechanisms should be treated as options for balanced funding of the transboundary management institutions in order to promote the common transboundary management of natural resources and support implementing the regionally coordinated policy.