Ocean-based industries like shipping, aquaculture, and wind energy are growing at an unprecedented rate resulting in challenges related to siting and environmental management. As marine aquaculture and other ocean-based industries continue to expand, robust marine spatial planning analyses that reconcile existing ocean uses and integrate pertinent environmental and planning data are critical for identifying compatible locations. In this study, a series of geospatial analyses were used for aquaculture siting within and around a heavily trafficked and highly utilized maritime port in the San Diego Bay area of California, USA. Using a centralized geodatabase representing key aquaculture planning spatial datasets, recommendations for specific areas for aquaculture were developed based on appropriate environmental conditions for candidate shellfish and algae aquaculture species culture systems. Areas that were known constraints were first identified to determine potentially usable areas for shellfish and macroalgae (i.e., seaweed) aquaculture using an exclusion analysis, a type of multi-criteria decision analysis, to eliminate all areas without compatibility. Within the remaining usable area, we further considered shellfish and macroalgae culture system-specific factors within a 'culture systems analysis' to determine where different culture systems have potential for success. This analysis provides a foundation of coastal intelligence for guiding the aquaculture industry and natural resource managers towards appropriate siting decisions. This study can serve as a replicable example of aquaculture spatial planning approaches for siting sustainable aquaculture and other blue economy industries.