The Gulf of Finland (GoF) suffers from a multitude of cross-border stressors generated by different kind of human activities. The project addresses the “common challenges in environment, public health, safety and security” and its thematic objective TO6 “Environmental protection, climate change mitigation and adaptation”. Countries surrounding the GoF have a common goal to protect its environment and to support the measures defined or taken to mitigate the harmful effects caused by human activity. The EU Strategy for the Baltic Sea Region and its Action Plan requires cooperative efforts on the transposition of EU Directives and defines the MSFD as the strategic, horizontal action. Implementation of MSFD in the EU Member States in the Baltic Sea area is not yet achieved within all descriptors – e.g. there is still a need for determination of good environmental status (GES) boundaries regarding harmful and emerging substances, and establish and implement relevant monitoring programs. The overall objective of the project is adaptation and implementation of uniform biological indicators for assessment and control of environmental quality in the eastern GoF. The development and harmonisation of marine monitoring and environmental status assessment between countries sharing the same sub-regions are essential. In particular, the exchange of information regarding the evaluation of pressures, joint attempts to fill in gaps regarding GES descriptors and boundaries, joint development of monitoring programs are needed. The proposed project is directly linked to the ongoing work in HELCOM and is the national (Estonian and Russian) and sub-regional (GoF) contribution rather than duplication regard to the assessment of the impact of harmful substances. The knowledge obtained in the frame of different previous independent and collaborative initiatives in the Baltic Sea region will be acknowledged and assessed/adapted for eastern GoF area. The main outputs of the project are the standard approach and strategies for transnational monitoring and assessment of emerging chemicals and harmful substances (HS) and their effects in the programme area and whole GoF. In particular: i) development and validation of techniques for monitoring impacts of selected HS on GoF benthic organisms; ii) compilation of pressure and impact maps based on modelling of the potential distribution of HS from different sources in the project area; iii) development of recommendations for regional (GoF) monitoring programme. The primary project beneficiaries are the environmental organisations at national (e.g. Ministry of Environment, National Environmental Boards), pan-Baltic and European levels (e.g., HELCOM), national political decision-makers (e.g. government commissions), administration bodies responsible for dealing with HS, Environmental NGOs, and last but not least, the public (through awareness raising). The main end-users of the project include private companies (such as wastewater and garbage disposal operators, ship operators, tourism operators, etc.) and municipalities (responsible for implementation of environmental policies at the local level). Activities include: i) the compilation of available data in Russia and Estonia and collection of additional data from hotspot areas in regard to the HS to evaluate the status of the GoF environment and assess the potential impact on the benthic organisms; ii) the study of priority substances included in the HELCOM Core Indicators list and pharmaceuticals considering their presence in the marine environment and estimating their impact on the biological processes of the key species of the eastern GoF; iii) modelling of the potential distribution of HS from different sources; iv) selection of most sensitive indicator species and biomarkers to develop the recommendations for regional (GoF) monitoring programme. The close cooperation of countries and institutions surrounding the eastern GoF will secure profound and uniform status and impact assessment results for the area and, in turn, contributes to the Baltic-wide MSFD implementation activities. Hence, the project contributes to policy-driven and solution-oriented cross-border studies for the protection of the GoF.