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.