Selection of a settlement site on a reef by coral larvae determines the corals ultimate survival, affecting the structure of coral communities and underpinning reef recovery from disturbance. Therefore, understanding the mechanisms underlying coral settlement is useful for predicting and managing the impacts of future disturbance regimes. An array of settlement cues and environmental conditions determine where coral larvae settle on a reef. How these processes interact to influence patterns of coral settlement remains largely unexplored, due to the difficulty in directly observing and measuring settlement in-situ. We developed a mechanistic simulation model to explore how three overarching factors (substrate attractiveness, hydrodynamics, and substrate configuration) interact to influence patterns of coral settlement over fine (centimetres to metres) spatial scales. Through scenario exploration, we found that interactions among these three factors can lead to contrasting patterns of settlement. By simulating common field survey methods (settlement tiles and quadrat sampling) we show that interactions among biological and environmental factors could lead to incorrect conclusions, regarding, for example, the substrates larvae prefer for settlement. Lastly, with a case study from Ningaloo Reef, we illustrate how the model can help explore the mechanisms underlying patterns of settlement within complex benthic communities.