Environmental and biological reef monitoring was conducted in Almirante Bay (Bahía Almirante) in Bocas del Toro, Panama, to assess impacts from anthropogenic developments. An integrated monitoring investigated how seasonal temperature stress, turbidity, eutrophication and physical impacts threatened reef health and biodiversity throughout the region. Environmental parameters such as total suspended solids [TSS], carbon isotopes (δ(13)C), C/N ratios, chlorophyll a, irradiance, secchi depth, size fractions of the sediments and isotope composition of dissolved inorganic carbon [DIC] of the water were measured throughout the years 2010 and 2011 and were analysed in order to identify different impact sources. Compared to data from Collin et al. (Smithsonian Contributions to the Marine Sciences 38:324-334, 2009) chlorophyll a has doubled at sites close to the city and the port Almirante (from 0.46-0.49 to 0.78-0.97 μg l(-1)) and suspension load increased, visible by a decrease in secchi depth values. Visibility decreased from 9-13 m down to 4 m at the bay inlet Boca del Drago, which is strongly exposed to river run off and dredging for the shipping traffic. Eutrophication and turbidity levels seemed to be the determining factor for the loss of hard coral diversity, most significant at chlorophyll a levels higher than 0.5 μg l(-1) and TSS levels higher than 4.7 mg l(-1). Hard coral cover within the bay has also declined, at some sites down to <10 % with extremely low diversities (7 hard coral species). The hard coral species Porites furcata dominated the reefs in highly impacted areas and showed a strong recovery after bleaching and a higher tolerance to turbidity and eutrophication compared to other hard coral species in the bay. Serious overfishing was detected in the region by a lack of adult and carnivorous fish species, such as grunts, snappers and groupers. Study sites less impacted by anthropogenic activities and/or those with local protection showed a higher hard coral cover and fish abundance; however, an overall loss of hard coral diversity was observed.

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