Worldwide, coral reef ecosystems are increasingly subject to natural and anthropogenic threats. Among human disturbances, chemical pollution is probably one of the most widespread. New Caledonia has a very speciose marine biodiversity, but due to intensive mining, increasing urbanisation and industrialisation, quantities of contaminants are present in the lagoon. This study aims to determine the concentration levels of metallic and organic pollutants in fish from New Caledonian coral reefs. Concentration levels of 12 metallic trace elements, 21 pesticides and 15 polychlorinated biphenyls (PCBs) were examined in the muscles of coral reef fish collected in 13 lagoon areas differently exposed to anthropogenic disturbances. The use of widely distributed year-round organisms can provide comparative data across the lagoon and fish are considered effective bioindicators for assessing contamination of marine ecosystems. Our results showed a wide dispersion of most contaminants over the whole New Caledonian coral reef lagoon and thus provide key baseline information to better interpret the impact of contaminants. They also highlight an urgent need for long-term monitoring of various contaminants on large spatial and temporal scales.