This paper aims to establish the connection between the theoretical and practical aims of the Office of the Hydrographer of the British Admiralty and Charles Darwin’s (1809–1882) work on coral reefs from 1835 to 1842. I also emphasize the consistent zoological as well as geological reasoning contained in these texts. The Office’s influences have been previously overlooked, despite the Admiralty’s interest in using coral reefs as natural instruments. I elaborate on this by introducing the work of Alexander Dalrymple (1737–1808), the (...) first hydrographer of the Admiralty and a figure who has flown under the radar of the history of coral reef theories. I show that Dalrymple introduced a unified account of coral reefs in which multiple features of the coral reefs, such as their shape, slope of the sides, ridges, channels, and elevation relative to the water, were all explained by the action of the winds and waves—and proposed that one could use these features to predict seafaring conditions around the islands. Then, I show that Darwin’s “Coral Islands” (1835) and his _Coral Reefs_ monograph (1842) spoke to these hydrographical issues and did so, at times, by way of zoological reasoning. It was, for instance, the coral behavior and the related notion of a zoological or botanical _station_ that ultimately proved the biggest blow to the Admiralty’s aim to use the coral reefs as instruments because it eroded many uniform predictions regarding the past or future of a coral reef. Connecting these themes leads us to a surprising conclusion: that Darwin’s theory of coral reefs, long a model instance of Darwin making uniform predictable inferences, was, in actuality, also his first formal encounter with something at times the entire opposite. (shrink)