Studies in aquatic systems have shown that habitat complexity may provide refuge or reduce the number of encounters prey have with actively searching predators. For ambush predators, habitat complexity may enhance or have no effect on predation rates because it conceals predators, reduces prey detection by predators, or visually impairs both predators and prey.

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The east coast of the Yucatan Peninsula, Mexico, consists of highly permeable limestone, such that surface flow and rivers are absent in this region. Extensive underground cave systems connect sink holes (cenotes) to submarine springs (ojos de aqua), which vent into the seagrass meadows of the adjacent oligotrophic coastal lagoons.

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The Bocas del Toro archipelago in the Caribbean sea on the northwest coast of Panama has high annual rainfall (> 3000 mm) and a mountainous watershed, resulting in high inflow of fresh water. The two main lagoons have different geologic structure and different inputs; while Bahia Almirante has carbonate sediment and a relatively small watershed, Laguna de Chiriqui has predominantly siliclastic sediment and a very large watershed.

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The often-rapid deposition of phytoplankton to sediments at the end of the spring phytoplankton bloom is an important component of benthic-pelagic coupling in temperate and high latitude estuaries and other aquatic systems. However, quantifying the flux is difficult, particularly in spatially heterogeneous environments.

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Tissue samples of liver and blubber were salvaged from fifty-three dugong (Dugong dugon) carcasses stranded along the Queensland coast between 1996 and 2000. Liver tissue was analysed for a range of heavy metals and blubber samples were analysed for organochlorine compounds. Metal concentrations were similar in male and female animals and were generally highest in mature animals.

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As part of the program monitoring the ecosystem health of Moreton Bay, Queensland, Australia, we developed a means for assessing ecosystem health that allows quantitative evaluation and spatial representations of the assessments. The management objectives for achieving ecosystem health were grouped into ecosystem objectives, water quality objectives, and human health objectives.

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We conducted high-resolution, underway sampling in April, July, and October for 6 yr (1995-2000) in the large estuary, Chesapeake Bay. This period included climatological extremes in freshwater inputs that strongly influenced both the overall stocks and spatial distribution of phytoplankton and zooplankton. Higher biomass of both phytoplankton and zooplankton occurred in springs, when freshwater input into Chesapeake Bay was above the average discharge.

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Management of coastal systems is becoming increasingly important, however understanding the process of effective management often remains elusive. This chapter contrasts examples of environmental problems and associated management in Moreton Bay, Australia, and Chesapeake Bay, USA. Targeted research in Moreton Bay identified specific issues which led to changed practices, while intense management and research in Chesapeake Bay has been unable to keep pace with increasing anthropogenic stress.

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Increases in contaminants associated with urban sprawl are a particular concern in the rapidly developing coastal areas of the southeastern United States. Polycyclic aromatic hydrocarbons (PAHs) are contaminants associated with vehicle emissions and runofff from impervious surfaces. Increased vehicular traffic and more impervious surfaces lead to an increased loading of PAHs into coastal estuarine systems.

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The abundance and productivity of benthic microalgae in coral reef sediments are poorly known compared with other, more conspicuous (e.g. coral zooxanthellae, macroalgae) primary producers of coral reef habitats.

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