Globally, cetaceans are considered sentinel species, as they play complex roles in the marine ecosystem and are excellent indicators of broader environmental change. The Galapagos Marine Reserve has been identified as an important location for marine mammals due to its highly productive waters and unique oceanographic conditions. However, limited information is currently available regarding habitat usage, health, and broader connectivity of Galapagos cetaceans with other populations in the Pacific. Focusing on blue whales (Balaenoptera musculus), bottlenose dolphins (Tursiops truncates) and orcas (Orcinus orca), this study utilized a wide range of methodologies including: photoidentification, body status assessment through video and photogrammetry, acoustic monitoring, tissue sampling, and the use of molecular and chemical markers. Results to date have identified important habitat hotspots for all three species and how this habitat usage is impacted by both large environmental (La Nina vs El Nino) and seasonal changes; generated baseline health data for local bottlenose dolphin populations; and have proven connectivity of blue whales that visit the Galapagos with both northern and southern Pacific populations. Information from this study will feed directly into management plans for the Galapagos Marine Reserve and the International Whaling Commission (IWC).