Spain’s extensive marine jurisdiction—comprising a continental shelf of approximately 100,000 km² and an Exclusive Economic Zone approaching one million km²—requires robust geospatial frameworks to support ecosystem assessment and marine policy implementation. This study presents GIS-based methodologies developed by the Spanish Oceanographic Institute (IEO-CSIC) within national initiatives such as LIFE IP INTEMARES project and the implementation of Marine Strategy Framework Directive (European Directive 2008/56/EC). The geospatial workflows developed for these initiatives integrates heterogeneous spatial datasets—such as multibeam bathymetry, acoustic backscatter, Remote Operated Vehicle (ROV) and towed-camera transects, sediment samples, oceanographic profiles, and species-habitat occurrence records—into a unified spatial analysis environment. Applied methods include digital terrain modeling, derivation of geomorphometric indices (e.g., slope, rugosity, curvature), image classification, and spatial statistics to quantify habitat extent, condition, and anthropogenic pressures. An integrated spatial analysis framework combining environmental and anthropogenic data is used to support zoning and management decisions within Marine Protected Areas (MPAs). Additionally, the deployment of WebGIS platforms facilitates data dissemination, iterative review, and stakeholder engagement, thereby enhancing transparency and accessibility. The resulting high-resolution maps, harmonized datasets, and computed spatial indicators—aligned with Marine Strategy Framework Directive (MSFD) descriptors such as habitat distribution (D1C4–C5) and seafloor integrity (D6C2–C3)—demonstrate how GIScience methods provide reproducible, decision-ready information to support the monitoring and management of Spain’s diverse marine ecosystems.