Transitional waters play a vital role in the ecological health and sustainability of coastal areas. According to European Union legislation, transitional waters are coastal water bodies influenced by freshwater flows but are partly saline due to their proximity to the sea. This study focuses on agricultural and forestry regions adjacent to transboundary transitional waters—i.e., areas where two or more countries share an estuary, tidal inlet, delta, or lagoon and have a contiguous border in their territorial waters. The objective of the study is to determine the patterns of riparian agroforestry around the transboundary transitional waters in Europe and the dependence of the sustainability of these agro-silvo-pastoral systems under stress on the overall cross-border coherence of the countries sharing these waters. The innovative methodology uses GIS and geostatistical interpretation to quantitatively interpret multi-layered spatial data from remote sensing and other sources. The article’s main finding is that in the direct catchment areas of 12 transboundary transitional waters in three European bioregions—the Baltic Sea, the Adriatic and Black Seas, and the Northeast Atlantic—the Dissimilarity Index values vary from 1.5% to 8.2% in different agroforestry systems.

Transboundary marine protected areas (TMPAs) are designed to conserve ecological features and processes that cross maritime jurisdictions. Still, effective designation requires integrating ecological evidence with diverse legal, spatial-planning, institutional, and management systems. This study develops an operational methodology for identifying, delineating, designating, and managing offshore TMPAs, grounded in a structured analysis of 288 scientific, legal, policy, technical, and institutional records in six languages. The resulting framework adapts established concepts into a 20-component, stepwise procedure that links ecological connectivity, spatial delineation, cumulative-pressure assessment, regulatory equivalence, governance, monitoring, and adaptive management. We appraised source authority, quality, relevance, and evidentiary strength using a source-specific hierarchy and treated uncertainty qualitatively at each stage. We tested the methodology in the South Baltic area, focusing on the Critically Endangered Baltic Proper harbor porpoise (Phocoenaphocoena), estimated at 400–500 individuals and exhibiting significant seasonal concentrations. Six analytical steps operationalized the framework, resulting in a preliminary spatial structure comprising three core areas, four ecological corridors, and three supporting areas across Lithuania, Poland, and Sweden. Legal and institutional comparisons revealed substantial compatibility through shared European Union (EU) and Helsinki Commission (HELCOM) frameworks, while also identifying differences in monitoring, permitting, fisheries regulation, enforcement, and management arrangements. The case study demonstrates the methodology’s internal coherence and operational applicability; however, it provides no evidence of ecological effectiveness, as the proposed TMPA has not been formally designated or prospectively monitored. Uncertainties persist regarding species distribution, cumulative impacts, final boundaries, and the implementation of equivalent measures across jurisdictions. Therefore, the model is reproducible and can practically support decision-making for structuring TMPA planning and identifying key ecological, legal, and governance requirements. The model’s future development should focus on testing in non-EU settings and areas beyond national jurisdiction.