Coral reefs are subject to extraordinary alterations under changing environmental conditions and increasing human resource use. Here we use a generic, spatially explicit, individual-based model to analyze fundamental interrelations and feedback loops relevant for coral reef dynamics, including recruitment, herbivory, benthic interactions, and fisheries. We assess the influence of three different fishing regimes (i.e. no-take, non-destructive and destructive fishing) and larval connectivity on the resilience of a coral reef community and explore respective thresholds. Simulation results show that changes in one of these parameters and a resulting imbalance in one feedback loop can disorder the whole interplay of regulating processes. Under many analyzed conditions alterations of herbivory or recruitment may induce a self-enhancing degradation of a coral dominated ecosystem state. Model results show that reefs can persist under non-destructive fishing with adequate larval connectivity but isolated reef sites are threatened at current modes of perturbations, because low larval recruitment does not allow for sufficient post-disturbance recovery. At high connectivity levels, fast growing species dominate and may displace other species. Often, these species increase three-dimensional structure, and thus, refuges for herbivores. However, this also reduces functional redundancy and if the dominant species (here Acropora muricata) is highly susceptible to thermally induced bleaching an extreme temperature event may cause overall coral extirpation and a regime shift to algal dominance. The model constitutes a virtual laboratory for reef studies, gives insights on how particular effectors may trigger cascades in the coral community, and hence highlights the necessity to analyze mechanisms not only separately, but within the whole system's context to fully grasp complex responses in ecosystems.