**3. Reefal bay sites**

Southeast of Jamaica, a 15 km stretch of coastline, the Hellshire east sector (Figure 2), consists of seven bays - four of which are reefal. Three bays were compared for their circulatory signatures – Wreck Bay, Engine Head Bay and Sand Hills Bay. Two of the three, Wreck Bay and Sand Hills Bay, have prominent reef parabola stretching between headlands with a central, narrow channel breaking the reef continuum. Wreck Bay, with its narrower channel, is more enclosed than Sand Hills Bay. Associated reefs are emergent and exposed, more so at low tide. Both reefal bays are separated along the coastline by Engine Head Bay, an open bay with no development of reef arms. Engine Head Bay was therefore considered as a control given it is non-reefal and its position exposes it to the same conditions as the two reefal bays.

A diurnal variation in the wind records is typical of the southeast coast of Jamaica (Hendry, 1983) due to the influence of the sea-land regime. The tidal range is microtidal ranging from 0.3 - 0.5 m with an annual mean of 0.23 m (Hendry, 1983) and demonstrating a mixed tidal regime. Tidally generated currents are therefore small in amplitude compared to winddriven currents. The wave climate of the southeast coast is influenced mainly by trade wind-generated waves that approach Jamaica from the northeast. Offshore waves impact the shelf edge off Hellshire from a predominantly east-south-easterly direction after undergoing southeast coast refraction. Swell waves approach the coast at a typical period range of 6-9 seconds, but these are soon affected by complex bathymetry. Wave decay occurs when the land-breeze emanates along the coast. The shelf along which these bays fringe are made up of basement rock composed of Pliestocene limestone eroded during low sea levels in the Pliestocene epoch. As a result, bathymetric highs are now shoals, banks, reefs and cays, and on the inshore, karst limestone relief facilitates freshwater sub-marine seeps into the bays (Goodbody et al., 1989).

The Hydrodynamic Modelling of Reefal Bays –

**4.1 Oceanographic and meteorological data collection** 

**Depth** 

3 Channel 4.0 20 Dec 2002 - 10 Jan

defining the reefal bay.

1) and outside of Wreck Bay.

**Mooring Location** 

**4.2 Hydrodynamic modelling** 

Placing Coral Reefs at the Center of Bay Circulation 159

an analysis of bay contraction and expansion due to circulation induced by the presence of the subtending reef, and ultimately the development of particular circulatory signatures

Bathymetric depth points were digitized from Admiralty bathymetric charts for the Hellshire coastline area and the entire South-East Shelf. For the finer-scale bathymetry required of the reef and bay areas, water depth (± 0.1 m) was measured to supplement the Admiralty data using an echo-sounder with Trimble Garmin GPS and post processed to account for tidal elevation differences from mean sea level. Wind speed (± 0.1 m s-1) and wind direction (± 0.1°) data were collected from the nearby Normal Manley International Airport weather center as continuous two-minute averages over the entire sampling period (1999 to 2003). Long-term current measurements for speed (± 0.10 cm s-1) and direction (± 0.1°) were recorded continuously by Inter-Ocean S4 current meters at four sites inside (Table

**(m) Deployment Dates Duration** 

1 Channel 4.0 24 May – 13 Jun 2000 3 5 min / 1 hr 2 Channel 4.0 11 Jul – 03 Sep 2000 7 5 min / 1 hr

4 Channel 4.0 14 Mar – 28 Mar 2003 1 1 min / 10

5 West Back-reef 2.0 11 Jul – 03 Sep 2000 7 5 min / 1 hr 6 East Back-reef 0.7 20 Jul – 01 Sep 2000 1 5 min / 1 hr Table 1. Deployment specifications for long-term field current data collection in Wreck Bay. Hydrodynamic model outputs were compared with these measurements for verification.

Hourly tidal amplitudes (± 1 mm) were calculated using Foreman's Tidal Analysis (Foreman, 1977) and Prediction Program, incorporating mean sea-level and tidal amplitude data over a 40-year period from Port Royal, a nearby tide station. Hourly incident wave height values (± 1 cm) used in the over-the-reef flow calculations were taken from Refraction-Diffraction (REFDIF) wave models (Kirby & Dalrymple, 1991) of the shoreline (Burgess et al., 2005). The deepwater wave climate obtained from JONSWAP (Hasselmann et al., 1973) analysis was used to run the REFDIF models in order to carry the deepwater waves from the continental shelf to the shoreline. Near-shore conditions were simulated at 50% occurrence (average conditions) and used as input into the hydrodynamic model.

A hydrodynamic model, RMA-10, was utilized to simulate the depth-averaged velocity field of the fore-reef and back-reef along with the shoreline flow under wind and tidal conditions typical of the Jamaican south-east coastal area. RMA-10 is a three-dimensional finite element model for simulation of stratified flow in bays and streams (King, 2005). The primary features of RMA-10 are the solution of the Navier-Stokes equations in three-dimensions; the use of the shallow-water and hydrostatic assumptions; coupling of advection and diffusion

**(wks) 0n / every** 

min

min

2003 3 1 min / 10

Fig. 2. Map showing the study site of three bays located on the Hellshire South East Coast of Jamaica. Wreck Bay and Sand Hills Bay are the two reefal bays under investigation, along with the open bay Engine Head Bay located between the other two.

Environmental stress studies conducted inshore and offshore these bays used plankton population size and species composition as indicators. Lowest values in biomass, primary production and density were recorded in the southernmost bays. These bays were therefore considered generally removed from the effects of the highly productive Kingston Harbour and Great Salt Pond waters to the north, with the exception of during flood occasions when elevated levels were recorded in the southernmost bay, Wreck Bay. The authors suggested the possibility of long retention times due to localized circulation (White, 1982; Webber, 1990). These results were of great interest given the implications presented for the protective role played by reefal bays as nurseries for the early aquatic stages of marine and terrestrial species; for the significance of its distance down-shore from the main harbor not inhibiting its eutrophication; and for sediment transport and exchange along the shoreline. In fact, physicochemical variables were also robust in characterizing the persistence of bay waters beyond the reef (Maxam & Webber, 2009). This indicated the need for appropriate numerical simulations to adequately describe the circulatory patterns in these bays - the findings of which are presented in this chapter.
