The paper presents a synthesis of results obtained by the INPOLDE international network created in the frame of MIS ETC 1676 Project (Romania, Republic of Moldova, Ukraine) concerning the monitoring of the ecological state of the border areas in Danube River and Danube Delta. Maps of pollution of water, sediments, soils and biota with trace metals and persistent organic pollutants (OCPs, total and individual PCBs and PAHs) were built using ArcGIS software. Also, preliminary results of the interdisciplinary studies performedin the first year of implementation of BSB27-MONITOX project on a large range of classes of toxic pollutants (TOXs) in an extended target area in the Black Sea Basin (BSB) (including NE part of Greece) are emphasized, as well as the assessment of toxicants’ impact upon human health using a risk calculator. The in-depth study of processes occurring in large, interconnected river basins and evaluation of people exposure to toxics can be accomplished only in partnership, through cooperation based on knowledge, exchange of good practices and interdisciplinary research, conducted only in transnational networks. One of the project goals are the integration of the chemical, radioactivity, biological and microbiological measurements, in order to establish the surface water quality classes for the first time based on an integrated ecotoxicological quality index, with important impact on human health. The set of ecological indicators which are routinely monitored in the frame of national monitoring systems does not include yet the emerging toxicants, such as pharmaceutical residues and metabolites, which are actually found in wastewater, surface water and groundwater. These are specified in EU-wide water monitoring Directive 2013/39/EU, which amended Water Framework Directive 2000/60/EC, and required a strategic approach to the pollution of water by pharmaceutical substances. In the future the national monitoring systems at EU level will have to implement such indicators for emerging contaminants which might be appropriate for prioritization. Moreover, at Union level, it is foreseen to set environment quality standards (EQS) for newly identified substances, revising EQS for some existing substances in line with the scientific progress, and setting biota EQS for some pollutants. The developed strategy, knowledge and common solutions for improved joint environmental monitoring will lead to a better informing of various stakeholders on the existent levels of TOXs in the region, together with the understanding of complex processes which take place during TOXs migration, accumulation in food chains, and understanding of the influence of toxicants and hazardous wastes on ecological state and human health. Acknowledgement: We acknowledge the funding from ENPI project code MIS ETC 1676 INPOLDE (2013-2015), Joint Operational Programme RomaniaUkraine-Republic of Moldova 2007-2013, and ENI project with eMS code BSB27 MONITOX (2018-2021), Joint Operational Programme Black Sea Basin 20142020.