Coral-associated viruses are a component of the coral holobiont that have received attention only relatively recently. Given the global increase in the prevalence of coral disease, and the lack of positively identified etiological agents for many diseases, these virus consortia require increased investigation. Little is known about the viruses that are naturally associated with coral reefs and how they are affected by the local environment. In the present study, a short-term analysis of viral consortia associated with the coral Montipora capitata in Kaneohe Bay, Hawaii, USA, was carried out to determine the environmental factors influencing their composition. Coral surface microlayer (CSM) and seawater samples collected at 4 sites with a range of environmental characteristics were analyzed using transmission electron microscopy (TEM), and relative abundances of virus-like particle (VLP) morphotypes were correlated with environmental measurements. Relative proportions of several CSM-associated VLP types, including phages and filamentous VLPs, were correlated with water temperature, turbidity and chlorophyll a levels. In seawater samples, turbidity and temperature showed the strongest correlation, altering the proportion of Podoviridae-like, Geminiviridae-like and putative Archaeal viruses, among others. Overall VLP consortium composition differed significantly between the CSM and seawater only at the more degraded sites, suggesting that human activity may be affecting coral reef-associated virus consortia.