Functioning as a flood regulator and a freshwater reservoir, the Prut River Headwaters Wetland, protected under the Ramsar Convention, is a crucial hub of biodiversity, including endemic, rare, and threatened species listed in the national and global Red Lists. There are gaps regarding site management issues, including a lack of an integrated wetland monitoring system. Therefore, the objective of this research was to organise the processes involved in the comprehensive planning of wetland monitoring. To achieve this, the study utilised the conceptual framework for monitoring developed by the expert group of the UNESCO Chair on Sustainable Management of Conservation Areas. By employing the method of information-analytical research, a model for the water monitoring programme focused on the Prut River Headwaters Wetland was developed. A combination of physicochemical and hydrobiological assessments has been designed and partly tested. The method was used to test the universality of the proposed methodology in a specific studied area that requires sustainable management, and for the purpose of studying the perspective of application to other wetlands or valuable natural complexes in nature conservation areas. For the Conceptual Phase of the monitoring programme development, the key elements of river basin management of the Water Framework Directive of the European Union were used in synergy with the provisions of the Ramsar Convention. During the Implementation Phase, field and laboratory investigations of water bodies within the testing site at seven control points were conducted (measuring physicochemical parameters with portable equipment). All parameters’ values were within the limits of permissible norms. A primary database of results stored in the SMART software has been created. The practical implementation of the water monitoring plan is anticipated to contribute to the evaluation of the wetland ecosystem’s condition and support the administration of the Carpathian National Nature Park in the sustainable management of the wetland area