A long-term study of the effects of nutrient enrichment on coral reefs (ENCORE Experiment) was carried out at One Tree Island (23°30′S; 152°96′E), Great Barrier Reef, between 1992 and 1996. The experiment involved the addition of water-soluble nutrients to 12 microatolls which contained a range of organisms and were situated within the larger lagoon. Three replicates of each of three nutrient treatments (nitrogen, phosphorus, nitrogen plus phosphorus) and an untreated set of three control atolls were prepared using the 12 selected microatolls. As part of the larger ENCORE experiment, changes in the chemical composition of the alcyonacean soft coral Sarcophyton ehrenbergi Marenzeller (Octocorallia: Alcyonacea), placed in the treatment microatolls, were monitored for a 1 yr period in an attempt to detect any responses attributable to nutrient enrichment. Multivariate analyses were performed to determine whether there were any patterns of response in the different nutrient treatments. At the level of individual metabolites, there were no clear treatment effects. However, the ratio of bioactive or stress metabolites (terpenes) to energy storage metabolites (lipids), referred to as the “physiological-change indicator”, revealed effects of nutrient enrichment. Nitrogen enrichment resulted in a trend towards higher physiological-change indicators than control or phosphorus treatments in the majority of cases, while phosphorus enrichment significantly decreased the ratio relative to controls. In most cases, the physiological-change indicator increased in soft soft corals relocated into contact with the scleractinian Pocillopora damicornis. The potential of soft corals to serve as indicators of a changed nutrient regime is discussed.