To evaluate the impact of land-based contaminants on benthic faunas, as part of the Land-Ocean Contamination Study (LOCS), a study transect was established in Jakarta Bay, Indonesia during the 1996 southeasterly monsoon. The transect extended 72 km between the city's main port, Tanjung Priok, and the Pilau Seribu Island chain in the Java Sea. The dissolved concentrations of Pb, Cu, Zn, Cr and Ni in seawater, in suspended particulate matter (SPM) and surficial sea bed sediments were measured along the transect at nine sites. In addition, metal concentrations were measured in tissues of the corals Goniopora lobata and Lobophyllia hemprichii at five sites, and of the green mussel, Perna viridis at six sites. An assessment of the impact of contaminants on the faunas was made using a biomarker approach, employing coral community analysis and lysosomal stability with Perna viridis. The results of the study showed two main trends. The distributions of metals dissolved in seawater, in SPM, and in the coral and mussel tissues were similar, and failed to show a consistent graded response from inshore to offshore sites. This suggests that the concentration of metals in waters is the primary route for metal uptake by the coral and mussel tissues. By way of contrast, a clear offshore increase in coral generic diversity, coral cover, coral colony numbers and neutral-red retention time (lysosomal stability) was observed, aug gesting increasing nearshore stress. Whilst the coral community stucture may reflect the seasonally-averaged metal distributions in the bay (shown by the metal content of sea bed sediments which increase shorewards), it is more likely that the coral community structure and lysosomal biomarker are responding principally to other nearshore stresses, such as sediment and nutrient loading of water (sewage) or, more likely, organic contaminants such as oils and other hydrocarbons. (C) 1999 Ifremer / CNRS / IRD / Editions scientifiques et medicales Elsevier SAS.