Marine coastal ecosystems (MCEs) play a critical role in climate change adaptation and human well-being. However, they face global threats from environmental pressures, both related to climate change (CC) and direct human impacts. Leveraging the increasing availability of geospatial data, this study explores Graph Neural Networks (GNNs) to assess cumulative impacts arising from human and CC related pressures on the Seagrass ecosystem in the Italian seas. Unlike traditional machine learning (ML) models with which they were compared in this study, GNNs incorporate the spatial component of data through graph structures. While experimental results demonstrate a modest performance improvement in GNNs, the study is constrained by limited data availability, preventing the exploration of the temporal component and physical laws representable through graph structures. Future efforts aim to collect higher-resolution spatial and temporal data, considering expressible environmental processes, to enhance model learning.