Ship-based oceanographic research related to coral reefs is carried on at AOML under the banners of several cooperating projects:

• The Florida Area Coastal Environment project operates a long-term monthly water quality-sampling program for the southeast Florida coast
• South Florida Ecosystem Restoration Program is a monitoring program focusing on physical oceanography, nutrient inputs and dynamics, and water quality for the Florida Keys, Florida Bay, and the southern portion of the West Florida Shelf
• FACE Florida Shelf eddy and internal wave studies collect ship- and mooring-based observations to characterize the physical oceanography and biogeochemistry of cyclonic vortices (mesoscale and smaller eddy features) as they interact with the Florida reef tract
• Caribbean Ecosystem Connectivity studies is a collaboration between AOML/PhOD (OAR) and SEFSC/ELH (NMFS) to quantify ichthyoplankton flux from spawning aggregation sites south of St. Thomas into the US and British Virgin Islands