The Black Sea is a semi-enclosed basin subject to intense anthropogenic pressures and transboundary pollution, making reliable and comparable monitoring data essential for large-scale environmental assessments. However, national practices differ considerably, hindering data integration and coordinated reporting under international frameworks. This study, conducted within the Horizon 2020 project “Advancing Black Sea Research and Innovation to Co-develop Blue Growth within Resilient Ecosystems” (BRIDGE-BS), evaluated pollutant surveillance methodologies with a focus on heavy metals and priority organic contaminants (polycyclic aromatic hydrocarbons, polychlorinated biphenyls, organochlorine pesticides). Standard Operating Procedures (SOPs) were collected from institutions across Black Sea countries and systematically compared for water, sediment, and biota matrices. The analysis revealed shared reliance on internationally recognized techniques but also heterogeneity in sediment fraction selection, digestion and extraction conditions, instrumental approaches, and quality assurance/quality control (QA/QC) documentation. To complement this assessment, an intercalibration (IC) exercise was organized through the QUASIMEME proficiency testing scheme, accompanied by a follow-up structured questionnaire sent to participant institutions. While individual results remain confidential, collective feedback highlighted common challenges in calibration, blank correction, certified reference materials (CRMs) availability, digestion variability, instrument maintenance, and the reporting of uncertainty and detection limits. Together, these findings confirm that harmonization in the Black Sea requires not only improved comparability of laboratory methods but also the future alignment of assessment methodologies, including indicators and thresholds, to support coherent, basin-wide environmental evaluations under regional conventions and EU directives.