Tropical Marine Ecology. Daniel M. Alongi

operate simultaneously in a water body. While bays and lagoons are tidal‐ or wave‐dominated systems, some coastal systems such as small, restricted inlets and large, semi‐enclosed bays, defy simple classification. Depending on several factors noted above, coastal embayments and bays and open coastal waters may or may not be stratified. Some waters are seasonally stratified.

      Coastal waters are greatly affected by the larger oceanic currents. Off East Africa, seasonal circulation patterns are generated by the behaviour of the ITCZ, which creates two distinct seasons, the NE and SE monsoons. During the southeast monsoon, coastal waters are characterised by cool water, a deep thermocline, high water column mixing and wave energy, and fast currents and low salinity due to high precipitation. These characteristics are reversed during the NE monsoon. The 1998 ENSO event produced heavy rains with resulting large sand bars deposited off river mouths, with a persistent decrease in salinity and temperature in inshore waters indicating a coastal boundary layer. ENSO rains also produced semi‐permanent flood channels serving as tidal inlets leading to tidal flooding of low‐lying areas.

      Inshore waters bathe, nurture, and are critical to the development and persistence of mangrove forests, coral reefs, and seagrass meadows. For example, in Gazi Bay, Kenya, a shallow, coastal bay, the main forcing function for water circulation are semi‐diurnal tides which generate strong reversing currents in the deep, narrow channels in the mangrove zone, but not in the seagrass and coral reef zones (Kitheka 1997). The peak ebb and flood currents are symmetrical in the seagrass and coral zones with equal duration and magnitude, unlike in the mangrove zone where tidal asymmetry results in ebb currents being slightly stronger than flood tides. Current speeds are slower in the seagrass and coral reef areas of the bay, but the tidal asymmetry in the mangrove zone promotes export of mangrove detritus to the seagrass zone. There is spatial variation in salinity due to evaporation, freshwater, and ocean water inflow. Ocean water is driven out of the bay during ebb tide. The mixing of the different water masses is especially noticeable in the dry season when the freshwater outflow is negligible. The influx of oceanic water into the bay often leads to a slight lowering of water temperatures. The coral zone is dominated by cooler temperatures, higher oxygen concentrations, and higher salinity due to turbulent mixing promoted by wave breaking. Overall, due to the orientation of the bay with respect to dominant tidal water circulation patterns, the lack of sills, and an open entrance, the rate of exchange between inshore and offshore waters is high, about 60–90% of the volume per tidal cycle (Kitheka 1997).

While each bay and embayment are unique, findings as in Gazi Bay have been found in other wet tropical regions where it is common to find a clear gradient from mangrove‐lined creeks to seagrass meadows to coral reefs with some mixing between estuarine and offshore waters (e.g. Sawi Bay in southern Thailand, Ayukai et al. 2000). Such physical gradients are even more distinct in the dry tropics where strong salinity gradients persist year‐round, especially in hypersaline lagoons. Good examples of such lagoons lie along the east coasts of Mexico, Brazil, and Sri Lanka. The northern Yucatán coastal zone of Mexico is a complex environment characterised by extreme evaporation and high seasonal rainfall (Enriquez et al. 2013). It has water exchange with numerous coastal lagoons ranging from brackish to hypersaline and receives intense groundwater discharges. Two main water masses persist along the coast: (i) the Caribbean Subtropical Underwater mass (CSUW) which is upwelled from the Caribbean and hugs the bottom along the coast and (ii) the Yucatan Sea Water mass (YSW) which is a mass of warm hypersaline water which originates in Yucatán due to high temperature and evaporation rates. Permeable karstic geology prevents the surface discharge of riverine water and instead water permeates directly to the aquifer and travels to the ocean via caves and fractures. Similarly, the Lagoa de Arauama is a hypersaline lagoon in coastal Brazil and persists due to semi‐arid conditions, but with a small drainage basin and a choked entrance channel (Kjerfve et al. 1996). For at least 450 a, the lagoon has been hypersaline, although the average salinity has varied in response to the difference between evaporation and precipitation. There is a long‐term trend of decreasing salinity due to constant pumping of freshwater from an adjacent watershed. A salt budget indicates that there is a delicate balance between the import of salt from the coastal ocean and eddy diffusive export of salt to the ocean.

      The hypersaline conditions of coastal lagoons can also be affected by climate change and by reduced river discharge due to anthropogenic alterations in water flow (Kennish and Paerl 2010). In the Puttalam Lagoon, a large, shallow water body on the west coast of Sri Lanka, salinity averages 37 with maximum values exceeding 50 during drought periods. The salinity regime is seasonal with rapidly decreasing salinities during the rainy season and increasing salinities during drought. Salinities were lower than oceanic water in 1960–1961 due to high freshwater discharge prior to human‐induced changes in river flow.

      Open coastal waters can also be hypersaline in the dry season. Salinities of 37 have been recorded in the Great Barrier Reef lagoon due to evaporation exceeding precipitation. These hypersaline waters are not flushed out by salinity‐driven baroclinic currents because lagoon waters are vertically well‐mixed and are transported by a longshore residual current, thus forming a coastal boundary layer (Andutta et al. 2011) exhibiting both longshore and cross‐shelf characteristics. The dynamics of the coastal boundary layer reaches steady‐state in about 100 days which is the average length of the dry season and differs from other coastal boundary layers that often are one‐dimensional with a dominant along‐channel salinity gradient. Although distinctive in its two‐dimensional nature, coastal waters of the tropics often have similar types of boundary layers with clear salinity gradients. These boundary conditions often disappear and break down completely during the wet season when heavy rains and storms help to mix inshore and offshore coastal waters.

      At the opposite extreme, continental shelf waters in the tropics commonly undergo ‘estuarisation’, especially near rivers during the wet season (Longhurst and Pauly 1987). This phenomenon occurs on the inner and middle portions of continental shelves and consists of low‐salinity waters usually exhibited as discrete plumes of discharged river water. The transport of river plumes onto continental shelves is a prime example of such ‘estuarisation’ and the exemplar is the Amazon plume, the low salinity (32–34) of which floats as far away as 2000 km from the mouths of the Amazon and Orinoco Rivers as a shallow plume of 20–30 m depth (Hu et al. 2004). ‘Estuarisation’ is also important in the Bay of Bengal, the Gulf of Panama, the South China Sea, and the Gulf of Guinea, in addition to discernible plumes proximal to other major tropical rivers. ‘Estuarisation’ on many tropical shelves is seasonal, depending on the onset of the monsoon, and the transition from unstratified to stratified conditions is sharp, delimited by a tidal front.

      Even small‐ and medium‐sized rivers can produce impressive shelf ‘estuarisation’. For example, in the Great Barrier Reef lagoon during and immediately after the wet season, diluted seawater migrates out to the Great Barrier Reef proper (Schroeder et al. 2012). These plumes can persist for weeks especially after a severe rainy season or a cyclone.

Subsurface water masses below the thermocline in the eastern tropical coastal oceans frequently contain an oxygen minimum layer. Several explanations have been offered to account for this poorly understood phenomenon, including minimal circulation or mixing of water to replenish oxygen consumed or that detritus accumulates in stagnant areas because of increases in water density with depth, leading to the depletion of oxygen (Stramma et al. 2008). Irrespective of the cause, low oxygen concentrations have important consequences for demersal fish and the benthic fauna (Chapter 7). Small rivers, creeks, and estuaries are also characterised by waters of low oxygen content with presumably similar biological consequences. These oxygen‐minimum zones are expanding as a direct result of global warming (Stramma et al. 2008).

      Coastal upwelling is another major feature of the tropical oceans. Such events occur at all latitudes, but within the tropics and subtropics, physicochemical differences between upwelled and surface water masses are greatest. Upwelling is dominant along the subtropical‐tropical boundary coasts of Peru‐Chile (Peru Current), Morocco‐Mauritania (Canary Current), Angola‐Namibia (Benguela Current) and California‐Mexico. Upwelling events also occur on the Malabar coast of India, off the Andaman Islands, Western Australia, the Gulf of Panama (the Costa Rica Dome),