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Disease is an ecological process that regulates hosts, but does not affect all host populations and communities uniformly. The extent to which populations and communities are affected by disease is determined by a suite of intrinsic factors such as host demography, susceptibility, and immunocompetence, as well as environmental extrinsic factors, which can alter host-pathogen interactions. Coral disease is a leading contributor to global coral reef decline, highlighting the importance of testing the role of intrinsic and extrinsic factors in disease affecting natural systems. Further, the ability of corals to respond to disease is influenced by the dynamics of innate immunity. The broad goals of this dissertation are to (1) address the patterns and processes of coral health and disease along the west coast of the Island of Hawai'i (WHI), which has some of the highest disease levels in the Pacific; and (2) investigate the temporal dynamics of the cellular immune response, using a Caribbean sea fan as a model system. Ecological processes including disease, competition for space, and predation strongly influence the health of coral communities. In Chapter 1, I characterize the spatial and temporal patterns in coral disease and other biological interactions, describes long-term changes in coral cover, and identifies sites of concern for management action along WHI. The spatial extent of disease in communities is determined by an integrated series of host population- and community-level processes. In Chapter 2, I test the effects of host demographics, coral species richness, predation and disease cooccurrence on the risk of three most common diseases affecting the scleractinian coral Porites. In addition to host ecology, disease is often influenced by environmental stress. In Chapter 3, I identify the risk factors contributing to dynamics of Porites growth anomalies by testing the correlation between prevalence, severity and linear extension, and ecological and environmental parameters across gradients of terrestrial input. Immune responses often determine an organism's success in pathogen and stress response. In Chapter 4, I use G. ventalina to characterize the temporal dynamics of cellular responses (granular amoebocyte aggregation and prophenoloxidase activation) to allogenic grafts in a series of laboratory and field experiments.