Coral reefs are important ecosystems in terms of their biodiversity and ecosystem functions. Particularly at local scales, coral reefs are vulnerable to natural and anthropogenic disturbances, leading to the degradation of reef health. Here, we employed two different methods to monitor reef health. First, we conducted line transect surveys to record the benthic community structure to infer ecological reef health. Secondly, trace metal concentrations in sediment samples and a bioindicator sponge species, Haliclona fascigera, were compared among sites to detect cryptic degradation and unknown sources of pollution. The study area comprised six reefs situated along the coast of Zanzibar's main agglomeration, Stone Town, and subject to different types of disturbances and conservation management schemes. Overall, coral reef health was found to decrease with increasing proximity to Stone Town, with living hard coral cover being particularly low on reefs closest to Stone Town, which coincided with greater fishing, tourism, and pollution pressures. Reef assessments based on trace metal analyses differed from the community structure surveys. All sites showed high levels of arsenic and cadmium contamination, with some samples revealing concerning levels of chromium, copper and zinc. The reefs differed significantly between each other in terms of trace metal concentration for both sediments (p = 0.031, PERMANOVA) and sponge samples (p = 0.001, PERMANOVA). Trace metal concentrations were not correlated with distance to Stone Town, highlighting the downstream effects of industrial and urban sewage on even remote reefs. Coral reef health assessment was found to be dependent on the survey method employed, which is why we recommend the combination of complementary methods.
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