Waterfronts represent a physical boundary between land and water masses, but also function as “membranes,” fluid zones of transition that regulate both ecological composition and urban development. In the Galápagos Islands, waterfronts simultaneously connect and isolate residents, to and from both the mainland and other islands in the archipelago. These relations are ever evolving, as port infrastructure, its usage and governance, and overarching contexts have shifted over time. In this chapter, we apply the “waterfront membrane” framework to a historical case study of Puerto Baquerizo Moreno—the capital of Galápagos Province and the main port on San Cristóbal Island. Our theoretical framework highlights the sophisticated organization and vulnerabilities of urban waterfronts, and we offer critical future areas of investigation relevant to the Galápagos Islands and other coastal states with similar fragile ecosystems.