Marine ecosystems are becoming increasingly vulnerable to cumulative anthropogenic effects and pressures. Therefore, various methodological approaches and tools have been designed to apply cumulative impact appraisal schemes and better assess the dynamics and interactions among pressures affecting marine ecosystems. This study aims to apply the Spatial Cumulative Assessment of Impact Risk for Management (SCAIRM) tool for the Black Sea coastal waters considering human activities, pressures, and effects on different ecosystem components coupled with one management scenario development for actual and new emerging sectors. According to the SCAIRM, the primary pressure on the marine ecosystem was identified as introducing or spreading non-indigenous species from shipping. Additionally, when considering cumulative impact, activities related to coastal defense and flood protection, particularly beach nourishment works, were found to have the highest impact. This is due to the cumulative scores associated with the physical loss from permanent alteration or removal of seabed substrates, and temporary or reversible physical disturbances to the seabed. The scenario development indicated that after shipping, oil and gas exploitation is anticipated to become the second-highest risk sector for additional impact in the Romanian Black Sea. Additionally, the increased military activities related to the war in Ukraine present escalating risks that must be considered in EBM strategies. The results assess the possible effects of human activities and the associated pressures to direct management toward achieving sustainability, biodiversity protection, and the marine ecosystem’s integrity.