Worldwide, coral reefs are challenged by multiple stressors due to growing urbanization, industrialization and coastal development. Coral reefs along the Thousand Islands off Jakarta, one of the largest megacities worldwide, have degraded dramatically over recent decades. The shift and decline in coral cover and composition has been extensively studied with a focus on large-scale gradients (i.e. regional drivers), however special focus on local drivers in shaping spatial community composition is still lacking. Here, the spatial impact of anthropogenic stressors on local and regional scales on coral reefs north of Jakarta was investigated. Results indicate that the direct impact of Jakarta is mainly restricted to inshore reefs, separating reefs in Jakarta Bay from reefs along the Thousand Islands further north. A spatial patchwork of differentially degraded reefs is present along the islands as a result of localized anthropogenic effects rather than regional gradients. Pollution is the main anthropogenic stressor, with over 80% of variation in benthic community composition driven by sedimentation rate, NO2, PO4 and Chlorophyll a. Thus, the spatial structure of reefs is directly related to intense anthropogenic pressure from local as well as regional sources. Therefore, improved spatial management that accounts for both local and regional stressors is needed for effective marine conservation.

Declining water quality is one of the main reasons of coral reef degradation in the Thousand Islands off the megacity Jakarta, Indonesia. Shifts in benthic community composition to higher soft coral abundances have been reported for many degraded reefs throughout the Indo-Pacific. However, it is not clear to what extent soft coral abundance and physiology are influenced by water quality. In this study, live benthic cover and water quality (i.e. dissolved inorganic nutrients (DIN), turbidity (NTU), and sedimentation) were assessed at three sites (< 20 km north of Jakarta) in Jakarta Bay (JB) and five sites along the outer Thousand Islands (20–60 km north of Jakarta). This was supplemented by measurements of photosynthetic yield and, for the first time, respiratory electron transport system (ETS) activity of two dominant soft coral genera, Sarcophyton spp. and Nephthea spp. Findings revealed highly eutrophic water conditions in JB compared to the outer Thousand Islands, with 44% higher DIN load (7.65 μM/L), 67% higher NTU (1.49 NTU) and 47% higher sedimentation rate (30.4 g m−2 d−1). Soft corals were the dominant type of coral cover within the bay (2.4% hard and 12.8% soft coral cover) compared to the outer Thousand Islands (28.3% hard and 6.9% soft coral cover). Soft coral abundances, photosynthetic yield, and ETS activity were highly correlated with key water quality parameters, particularly DIN and sedimentation rates. The findings suggest water quality controls the relative abundance and physiology of dominant soft corals in JB and may thus contribute to phase shifts from hard to soft coral dominance, highlighting the need to better manage water quality in order to prevent or reverse phase shifts.

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