Abstract Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology , 27: 261–269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology & Evolution , 4: 502–511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year‐long in‐natura study—incorporating sampling at diel, monthly, and seasonal time points—in which we compared corals from an urban area to corals from a proximal non‐urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long‐term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.