Tidal and Seasonal Variability Circulation Patterns in the Coral Reef

System, Berau Continental Shelf, East Kalimantan

Ayi Tarya

, A. J. F. Hoitink

and M. van der Vegt

Department of Oceanography, Faculty of Earth Sciences and Technology, Bandung Institute of Technology,

Bandung 40132, Indonesia

Hydrology and Quantitative Water Management Group, Wageningen University,

Droevendaalsesteeg 3, 6708 PB Wageningen, The Netherlands

Institute for Marine and Atmospheric Research Utrecht/IMAU, Department of Physical Geography, Utrecht University,

P.O. Box 80115, 3508 TC Utrecht, The Netherlands

Keywords: Tidal Variability, Seasonal, Coral Reef System, East Kalimantan.

Abstract: The present study examines tidal and seasonal circulation dynamics in the coral reefs, Berau Continental

Shelf, East Kalimantan which exist multiple reef passages by using analysis field data and a three-dimensional

hydrodynamic model. The predicted M2 tidal currents, velocities, salinity profiles and sea surface elevation

show a good agreement with observed. The model results demonstrate the reef-scale circulation patterns on

tidal to monsoonal variation. On the seasonal timescale, the circulation patterns strongly reflect the Monsoon

seasonality. The coral reefs exposed by river plume when southwesterly wind prevailed. In this period, the

vertical structure of salinity displays a thin stratified water column. The velocity profiles exhibit a classical

estuarine circulation with outflow at the top layer and inflow at the bottom layer. For the tidal periods, the

tidal currents present complex structures at the reef passages and exhibit the tidal eddies generated by

irregularities reef gaps. The flow in the centre of the reef passage is often opposed to the flow near the reef

boundaries. A mixed vertically water column occurs during spring tide. During neap tide, the water column

structures form a thin stratified on top layer and a classical estuarine circulation for velocity profiles. At the

cross-section of reef passages, the lateral velocities develop the two-cell circulation with upward flow at reef

shores and an axial convergence (downward flow) at mid-reef passage during flood and reverse pattern during

ebb. At the reef slope of continental shelf edge, the model results suggest an upward flow that generated by a

Bernoulli effect during flood tide, which may be lifting the nutrient-rich water to the reef passage.

1 INTRODUCTION

Circulation dynamics in coral reef systems can be

driven by a number of forcing functions such as

waves, tides, wind and density gradients (Andrews

and Pickard, 1990; Kraines, 1998; Wolanski, et.al,

1988; Wolanski and Thomson, 1984; Hoitink, 2004;

Monismith, et.al, 2006). The associated length scales

are ranging from an individual coral colony to the

reef, island, and basin scale (Monismith, 2007). In

coral reef systems, the hydrodynamics play a crucial

role in ecological and biogeochemical processes

including dispersal of larval fish and corals (Black,

1993), supply of nutrients to reef organisms (Falter,

et.al, 2004), renewal of oxygen (Nakamori, et.al,

1992), delivery of phytoplankton (Yahel, et.al, 1998),

the dynamics of zooplankton (Yahel, et.al, 2005),

transport of terrigenous sediments (Storlazzi, 2004;

Haitink and Hoekstra, 2003), and the distribution of

mobile reef fishes (Clarke, et.al, 2005). Therefore, to

understand biological and ecological patterns and

function in coral reef systems, it is critical to identify

the circulation and transport processes.

The importance of wind and waves on circulation

patterns in coral reef environments has been

investigated extensively (e.g. Wolanski and

Thomson, 1984; Hoitink and Hoekstra, 2003;

Wolanski and Pickard, 1985; Yamano, et.al, 1998;

Presto, et.al, 2006; Kench, et.al, 2009). Wolanski and

Thomson (1984), Wolanski and Pickard (1985))

reported that the subtidal sea level dynamics and

currents are found to be highly coherent with the local

wind variability in the Great Barrier Reef. Trade

wind-driven processes are found to be the dominant

Tarya, A., Hoitink, A. and van der Vegt, M.

Tidal and Seasonal Variability Circulation Patterns in the Coral Reef System, Berau Continental Shelf, East Kalimantan.

DOI: 10.5220/0008372500090015

In Proceedings of the 6th International Seminar on Ocean and Coastal Engineering, Environmental and Natural Disaster Management (ISOCEEN 2018), pages 9-15

ISBN: 978-989-758-455-8

control for circulation and sediment dispersal on the

shallow, broad reef flats off southern Molokai,

Hawaii (Presto, et.al, 2006). The interaction between

tides, local bathymetry, coral reef shape, size and

spacing can result in periodic reef-scale flow patterns,

featuring tidal jets, eddies and circulation cells across

the reef passage (Wolanski, et.al, 1988; Wolanski and

Hamner, 1988; Young, et.al, 1994; King and

Wolanski, 1996). Using a regional model with a 2 km

resolution, (King and Wolanski, 1996) established

that such local features result from flow interaction

with complex topography. Local residual flows may

impact the fate of river effluents reaching coral reef

areas, which pose a contemporary threat to the health

of coral reefs. The reef chain under study features a

monsoonal pattern exposed to river plume spreading

(Tarya, et.al, 2015). (Tarya, et.al, 2018) revealed that

the coastal ecosystem communities at the BCS are

most exposed to low salinity when southwesterly

winds are prevalent, at neap tide. These findings

motivate the present study to further investigate the

circulation patterns on the coral reef-scale and on the

intratidal periods. In this contribution, we focus on

the detailed circulation processes across the reef

passages at the BCS, over a tidal cycle.

Figure 1: Map of the Berau barrier reef (a), showing depth

in meters. Berau Continental Shelf and the position of the

Berau barrier reef (b) and map of Indonesia (c). The dashed

red line Te-Tf and Tg-Th indicates the location of the depth

profile across-northern passages (d) and across-southern

passages (e), respectively. The dashed red line Ta-Tb and

Tc-Td are depth profile along the northern (f) and southern

passage (g), respectively. The red circles indicate fixed

ADCP and CTD stations near Derawan Island. Red

triangles indicate fixed ADCP stations at Masimbung inner

shelf and Masimbung outer shelf. The red square indicates

the sea surface elevation at CG station.

2 STUDY AREA

The Berau barrier reef is a juxtaposition of permanent

and periodically exposed reef islets at the edge of the

BCS, East Kalimantan (Figure 1). It features a

species-rich coral reef ecosystem (Hoeksema and

Suharsono, 2004; Renema, 2006; Renema, 2006;

Voogd and Becking, 2009), which is part of the Coral

Triangle in the central Indo-West Pacific (Tomascik,

et.al, 1997; Hoeksema, 2007). The islets are

elongated in the along-shelf direction, and are

separated by 0.8 to 3 km wide passages with depths

between 5 and 50 m (Figure 1d and 1e). In the

northern areas of the barrier reef, passages can be as

deep as 50 m, whereas in the south the depths in the

passages are less than 15 m. The reef flats emerge

only during low water spring tide. The inner shelf

separating the barrier reef from the Berau estuary is

about 30 km wide. Depths in that area are typically

around 30 m. Figures 1f and 1g show typical bottom

profiles across the passages. The northern passage has

a depth of about 50 m and in the southern passage, the

depth is in the order of 10 m or less. Further seaward,

the shelf break is located with a very steep bottom

slope. Corals are found across a water gradient from

fluvially influenced to fully oceanic conditions.

Inshore, reefs feature a relatively low coral cover,

with high densities of filter feeders such as sponges,

soft corals and crinoids (Renema, 2006). Coral rubble

in the areas close to the mainland is often covered by

fine mud and silt, with a terrigeneous origin. The

outer shelf reef is comprised of diverse reef types,

dominated by dense stands of corals and coarse sand

(Renema, 2006).

3 METHODS

3.1 Field Surveys

Flow velocities, sea surface elevations and

meteorological data were gathered during three field

campaigns in the period between September 2006 and

February 2008. Acoustic Doppler current profiler

(ADCP) surveys were collected with an RD

Instruments Broadband 1200-kHz ADCP, pinging at

2 Hz over 60 depth cells with a size of 0.5 m. The

ADCP transducer was mounted approximately 0.5 m

below the sea surface, and had a 0.5 m blanking

distance. The survey boat sailed at a speed of

approximately 2 m/s. As a result of the extremely

clear water conditions, ADCP backscatter rapidly

decreased with depth, limiting the observation range

to 15 m. Repeated transect measurements were

carried out across several cross-sections in a northern

and a southern reef passage. The track length was

chosen to include the largest number of cross-sections

that could be covered within about 1.5 hours, such

ISOCEEN 2018 - 6th International Seminar on Ocean and Coastal Engineering, Environmental and Natural Disaster Management

that each location on the track was repeated 10 times

within an M2 tidal cycle.

3.2 Hydrodynamic Model

The simulations were performed using the Princeton

Ocean Model (POM) (Blumberg and Mellor, 1987).

This is a three-dimensional, terrain-following finite

difference model based on sigma-coordinates, which

solves for water level, velocity, temperature, salinity,

turbulence kinetic energy and macro-scale turbulence

properties. The model adopts the turbulence closure

scheme by (Mellor and Yamada, 1982) to

parameterise vertical mixing and uses the

(Smagorinsky, 1963) diffusivity formulation for

horizontal diffusion. POM has been used in a variety

of oceanic and coastal applications including coral

reef systems (e.g. Ezer, et.al, 2005; Ezer, et.al, 2010).

The local model was nested in the existing

regional model by (Tarya, et.al, 2015) and features a

200 × 200 horizontal orthogonal curvilinear grid, with

a resolution ranging from 40 m at reef passages to

about 100 m at the outer shelf. 15 sigma levels were

defined at 2, 4, 6, 8, 10, 15, 25, 40, 50, 60, 70, 80, 90,

95 and 100% of the water depth. The depth of each

grid cell in the reef environment was interpolated

from bathymetry data measured during a field survey.

Depths in the parts of the domain that cover the shelf

and deep sea areas were derived from the Indonesian

Naval Hydro-Oceanographic Office (DISHIDROS).

A computational time step of 1 s was used for the

external mode, while the internal mode time step was

set to 10 s.

Sea surface elevation, currents, temperature and

salinity at the open boundaries were obtained from

the BCS regional model (Tarya, et.al, 2015). The sea

surface elevation and momentum variables were

implemented adopting the radiation condition of

(Orlanski, 1976) that allows incoming waves to freely

propagate into the domain, and pass out to the exterior

without any reflection back into the computational

domain. Time-variable winds are imposed uniformly

over the domain model. Hourly observations were

collected from Derawan station (see Figure 1) for

the period from March 2007 to January 2008,

while the wind data for the period February 2006 to

January 2007 was extracted from the NCEP

reanalysis database, provided by the National

Oceanic and Atmospheric Administration (NOAA)

(www.esrl.noaa.gov/psd).

Figure 2: Modelled and observed comparison for surface

layer (a and b), depth-mean (c and d) and bottom layer (e

and f) velocity for east (left panels) and north direction

(right panels) components of the flow near Derawan (see

Figure 1).

4 RESULTS

4.1 Comparison of Model Results and

Measurements

Modelled sea surface elevation, velocity profiles and

salinity were compared with observations to evaluate

the performance of the model. Figure 2 present time-

series of observed and modelled velocity for the

surface layer, the depth-averaged and the bottom

layer near Derawan Island. Model performance is

quantified by the Mean Absolute Error (MAE), the

Root Mean Square Error (RMSE) and the Correlation

Coefficient (CC) (Liu, et.al, 2009; Vested, et.al,

2013) as displayed in Table 1. The CC score between

modelled and observed values of sea surface

elevation is 0.95. RMSE and MAE are 0.08 m and

0.09 m, respectively. The modelled velocity profiles

reveal a CC score above 0.86; MAE and RMSE are

lower than 0.14 m/s. For the salinity profiles, the CC

score is above 0.86. MAE and RMSE are less than 0.1

psu. Overall, model-data comparisons have shown

that the model performs well in reproducing the

observations.

Tidal and Seasonal Variability Circulation Patterns in the Coral Reef System, Berau Continental Shelf, East Kalimantan

Table 1: Validation model results with observations based

on the Mean Absoulte Error (MAE), Root Mean Square

Error (RMSE) and Correlation Coefficient (CC).

Location Parameter Layer Period MAE

RMS

Derawan Salinity Surface

8 Aug

0.04

psu

0.08

psu

0.87

Middle

8 Aug

0.04

psu

0.07

psu

0.91

Bottom

8 Aug

0.03

psu

0.05

psu

0.95

Salinity Surface

Aug

0.05

psu

0.06

m/s

0.94

Middle

Aug

0.03

psu

0.05

m/s

0.93

Bottom

Aug

0.03

psu

0.04

m/s

0.95

Derawan

East

velocity

Surface

7-17

Aug

0.07

m/s

0.09

m/s

0.93

Middle

7-17

Aug

0.10

m/s

0.13

m/s

0.84

Bottom

7-17

Aug

0.05

m/s

0.04

m/s

0.96

North

velocity

Surface

7-17

Aug

0.04

m/s

0.05

m/s

0.92

Middle

7-17

Aug

0.05

m/s

0.06

m/s

0.81

Bottom

7-17

Aug

0.03

m/s

0.03

m/s

0.94

4.2 Seasonal Circulation Dynamics

The Figure 3 describes the mean circulation and

salinity patterns for the surface layer demonstrate a

monsoonal pattern. During the transition from the

Northwest to the Southeast Monsoon (Figure 3a), the

south westerly wind generates the residual northeast

flow toward the coral reefs. The vertical structure of

velocity exhibits a classical estuarine circulation with

offshore flow in a low- density top layer and inshore

flow in the bottom layer, for both reef passages

(Figure 4).

During the Southeast Monsoon (Figure 3b), the

steady southerly winds drive northward residual

currents aligned with the barrier reef. In this period,

there are no freshwater influences in the barrier reef

area. The wind changes from southerly to northerly

Figure 3: Seasonal pattern of salinity and velocity in the

surface layer during transition from the Northwest to the

Southeast Monsoon (a), the Southeast Monsoon (b), the

transition from the Southeast to the Northwest Monsoon

(c), and the Northwest Monsoon (d).

Figure 4: Modelled mean velocity profiles during the

transition from the Northwest to the Southeast Monsoon in

cross-sections of the northern reef passage between

Derawan and Masimbung (a) and the southern reef passage

between Masimbung and Pinaka (b). The bottom panels

show the corresponding salinity field. The locations of the

transects are indicated in the top plots.

ISOCEEN 2018 - 6th International Seminar on Ocean and Coastal Engineering, Environmental and Natural Disaster Management

during the Southeast to Northwest Monsoon

transition. This shifts the surface circulation patterns

from northward to southward flow (Figure 3c).

Subsequently, the currents through the reef passages

weaken and reverse from offshore to inshore.

Although the wind is relatively weak during this

period, it is effective in dispersing the river plume to

the south of the BCS (Tarya, et.al, 2010) and thus the

reef passages present vertically uniform seawater and

homogeneous velocity profiles directed inshore.

During the Northwest Monsoon (Figure 3d), the mean

circulation and mean salinity patterns are similar to

those in the transition period, but the flow is stronger

due to increased northerly wind speed.

4.3 Seasonal Circulation Dynamics

4.3.1 Horizontal Structures

Figure 5 displays depth-mean instantaneous velocity

patterns over a tidal cycle in two reef passages. The

asymmetric topography of the barrier reef causes

flood flow patterns to deviate from the ebb flow

patterns. This holds especially in the northern passage

(Figure 5 left panels), where several eddies are

created in the lee of reef outcrops. The flow in the

center of the reef passage is often opposed to the flow

near the reef boundaries. The reef waters are subject

to tidally-driven flow separation and transient eddy

development, as observed previously by (Pingree,

1978; Black and Gay, 1987; Signell and Geyer,

1991). Reef outcrops can act as headlands, generating

an adverse pressure gradient where the laterally

confined flow diverges and decelerates again.

4.3.2 Vertical Structures

Figures 6 illustrates streamwise and lateral velocities

for peak flood and peak ebb during spring and neap

tides, across the northern reef passage. The flow

structure presents a distinctive temporal evolution

over a tidal cycle. During spring tide, along-channel

velocities attain magnitudes above 1 m/s, which

causes strong vertical mixing, preventing

stratification. The lateral flow structure exhibits a

two-cells pattern with surface flow convergence

toward the middle of the passage and bottom flow

divergence. The secondary circulation reverses

during ebb. For neap tide, along-channel velocities

become weaker and allow stratification. The same

two counter-rotating cells of lateral circulation on

either side of the channel axis are evident at neap tide.

However, the flow magnitude is reduced compared to

spring tide conditions.

Figure 5: Depth-mean velocity structure during spring tide

at early flood (a,b), maximum flood (c,d), late flood (e,f),

early ebb (g,h), maximum ebb (i,j), and late ebb (k,l) in

northern (left panels) and southern reef passages (right

panels).

Figure 6: Flow velocities (a,c,e and g) and salinity (b,d,f and

h) for a cross-section in northern passage during spring tide

and neap tide. The transect is the same as in Figure 5. Colors

in the left panels indicate along-reef velocity in the passage.

Red indicates offshore flow and blue represents flow

toward the inner shelf. Arrows display lateral and vertical

velocity components. Color in right panels indicates

salinity.

Tidal and Seasonal Variability Circulation Patterns in the Coral Reef System, Berau Continental Shelf, East Kalimantan

5 DISCUSSION

The south westerly wind during the transition period

drives a north eastward flow that pushes the river

plume to the barrier reef and results in reef exposure

to terrestrial contaminants. The Northwest Monsoon

induces a southward residual current that conveys

seawater from the open sea. This sequence is essential

for flushing of poor quality water. The importance of

wind-driven flow to the survival of corals was

previously demonstrated by (Kitheka, 1997), who

found that the onshore wind-driven flow traps the

brackish plume along the south- western coast of the

Gazi Bay in Kenya. This ensures that turbid water

from the rivers does not reach the coral reef

ecosystem in Gazi Bay. Wind induced circulation

patterns that play a role in flushing of poor quality

water was also reported for the Florida Keys coral

reefs (Smith, 2009).

The present study highlights two important

processes in coral reef circulation. First, coral reefs

that possess a highly irregular shoreline and bottom

generate eddies (Pingree and Maddock, 1978). Over

time these eddies grow and decay with tidal phases

and result in a non-uniform residual flow field. This

asymmetry in flow creates a potentially longer

retention time of water masses in certain areas around

the reef. The generation of the eddies has been

proposed as an important physical mechanism that

may limit the dispersion of larvae due to the

recirculating properties of the water masses that trap

and conserve propagules near reefs.

Second, lateral velocity shear in a reef passage

with longitudinal density gradients produces the two-

cell secondary circulation patterns that form a mid-

channel axial convergence and divergence zone over

a tidal cycle (Nunes, 1985). The present results

highlight the secondary flow structure in the reef gaps

during ebb tide and suggest that the water masses of

the river plume may be advected in a downward

direction leading to additional exposure of the reefs.

This process occurs at the shallow reef gaps during

neap tides when stronger buoyancy forcing exists.

6 CONCLUSIONS

Coral reefs that possess a highly irregular shoreline

and bottom generate eddies. Over time these eddies

grow and decay with tidal phases and result in a non-

uniform residual flow field limiting the dispersal of

larvae. Lateral velocity shear in a reef passage with

longitudinal density gradients produces the two-cell

secondary circulation patterns that form a mid-

channel axial convergence and divergence zone over

a tidal cycle.

ACKNOWLEDGEMENTS

This work was partially funded by Research,

Community Service and Innovation, Bandung

Institute of Technology (P3MI-ITB 2018). The

fieldwork was part of the East Kalimantan

Programme (EKP) funded by WOTRO Science for

Global Development, a division of the Netherlands

Organisation of Scientific Research (NWO) under

grants WT77–204.

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Tidal and Seasonal Variability Circulation Patterns in the Coral Reef System, Berau Continental Shelf, East Kalimantan