The three-dimensional form of a coral reef emerges from thousands of years of ecological interactions between reef-building organisms and their environment. Time integrates those interactions, such that the predominant ecological processes are distilled into reef form, often as striking geometric patterns. Several of these patterns have a fractal appearance, exhibiting nested, scale-invariant structure. Cellular reefs are one fractal reef morphotype, characterised by the presence of subcircular, bowl-shaped, depressions (‘cells’) within the reef network. Cell diameters range from approximately 10 metres to 1 kilometre, the larger cells being compound structures containing multiple smaller cells. The common attribute shared by cellular reefs of all scales is an abundance of staghorn Acropora. Staghorn’s fast growth, fuelled by a correspondingly fast metabolism, allows them to rapidly fill lagoons, but leaves them vulnerable to reduced water flow as their own growth begins to impede lagoonal circulation. This article outlines a conceptual model of multi-scale cellular reef development, based on water quality and coral distribution data from the cellular reefs of Western Australia’s Houtman Abrolhos Islands. The key process in the model is density-stratification of the water column during extended periods of warm, calm, weather. Warm water in the shallows traps stable pools of cooler and denser water at depth. The trapped water is rapidly depleted of oxygen, which causes extensive mortality among staghorn colonies. This initiates a negative feedback process in which ongoing growth of colonies above the stratification boundary further reduces water circulation at depth, such that subsequent stratification events kill increasingly larger areas of the reef, eventually producing massive, stagnant cells in which few corals can survive. Investigating the many other reef patterns may provide similar insights into the predominant natural ecological processes occurring on those reefs.