Scleractinian corals, which create complex three-dimensional carbonate structures, are the foundation of coral reef ecosystems. There are a variety of coral growth forms or ‘morphologies’ that have distinct advantages and disadvantages when corals compete for space and light, and when they are exposed to hydrodynamic disturbances. We developed a novel three-dimensional functional-structural model, Coralcraft, to investigate how hydrodynamic disturbances (of different frequencies and intensities) influence coral communities. Using five common coral morphologies—encrusting, hemispherical, tabular, corymbose and branching—Coralcraft tracks the temporal dynamics of simulated coral communities. Six metrics are considered: (1) the number of colonies, (2) the percentage cover and (3) the volume of each morphology; (4) the structural complexity (rugosity) and (5) the total coral cover of the community; and (6) the diversity of morphologies in the community as calculated according to metrics (1)–(3). Frequent high intensity disturbances caused the greatest reduction to the structural complexity and morphological diversity of simulated communities, with some variation depending on the metric used to calculate diversity. Conversely, scenarios of no disturbance or infrequent disturbance (of low or high intensity) led to communities with higher structural complexity and a higher diversity of morphologies. These results indicate that disturbance frequency may play a greater role in eroding structural complexity and diversity than disturbance intensity. Importantly, given that the scientific coral reef literature generally uses percentage cover, the other metrics we considered—number of colonies, volume, rugosity and diversity—captured the dynamics of impact and recovery from disturbance in subtly different ways. While there are many models for corals, Coralcraft is the first to model the temporal dynamics of three-dimensional growth, competition and response to disturbance in a community with different coral morphologies.