Environment and development
in coastal regions and in small islands
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Coastal region and small island papers 6

Biophysical assessment of Jakarta Bay and Seribu Islands 


Jakarta Bay is located north of the Indonesian capital city, Jakarta. It is a shallow bay, with an average depth of about 15 m, an area of 514 km2, and a shoreline about 72 km long. On its eastern and western sides, the bay is bound by two capes, Tanjung Karawang and Tanjung Pasir, respectively. The bay receives highly polluted water from the nineteen rivers that run through the Jakarta Metropolitan Area.

Kepulauan Seribu is an archipelago within Jakarta Bay. This chain of offshore islands stretches some 80 km in a northwest to southeast line and 30 km from east to west (see Figure 1). Although the name Kepulauan Seribu means 'thousand islands', there are currently 105 in all, so the island group is referred to in this report as the Seribu Islands. On average, the islands are smaller than 10 ha and less than 3 m above sea level. Administratively, the Seribu Islands are under the authority of the Jakarta City government (Daerah Khusus Ibukota Jakarta – DKI). The archipelago is used for many purposes: tourism, sand mining, off shore oil exploration, sailing and fishing.

Human activity in and around the bay started thousands of years ago. Initially, the bay was used only for fishing, although it is probable that some shipping took place along the coast. At the beginning of the colonial period, Jakarta Bay was one of the first landing points for foreign powers. The current harbours of Tanjung Priok and Sunda Kelapa were first used more than 300 years ago. In former times, some of the islands in the bay were used for quarantine. Within recent decades many of the people living in and around the bay have been involved in fish and shrimp farming. The sea floor and reefs close to Jakarta have been dredged for landfill, and thousands of hectares around the bay have been trans formed into fishponds, luxury residences, industrial zones and fishers' kampungs (residential neighbourhoods). Some of the islands are national park wildlife refuges, others have been developed as tourist re sorts or residential communities for Jakarta. Further offshore, to the northwest of the reef tract, a major oil field exists and oil is being extracted.

Jakarta Bay is important for a number of human activities which contribute significantly to the economic development of the region. However, the high population growth rate, together with the expansion of Jakarta City during the second half of the 20th century, have led to serious pollution and over-exploitation of coastal and marine resources, thus threatening the sustainability of the marine environment. Within Indonesian coastal waters, Jakarta Bay has undergone some of the most drastic changes over the last few decades.


2.2.1. Disappearance of islands

Several of the Seribu Islands disappeared in the 20th century mainly as a result of human activities. Coral reefs were removed at Air Kecil and Ubi Kecil Islands, and as a result of subsequent erosion, both islands have now disappeared. Ubi Besar Island is eroding rapidly as the reef around it is dredged, see Figure 2. Willoughby et al. (1998) reported that three islands disappeared below sea level between 1985 and 1995.

Figure 2.
Change in
Ubi Besar Island
Stoddart, 1986)

2.2.2. Status of coral communities of Seribu Islands

Much of the information described in this and the following section (2.2.3) has been derived from the proceedings of a 1995 'Coral reef evaluation workshop, Pulau Seribu' (UNESCO, 1998).

The corals and reefs of the Seribu Islands were first described in detail by Umbgrove (1928, 1929, 1939) and Verwey (1931), who found them in generally good condition in the 1920s, although some human influence was already apparent on nearshore reefs. With the rapid expansion of Jakarta, increasing use of the resources of the reefs and islands of the Java Sea occurred (Harger, 1986; Tomascik et al., 1994).

A long-term coral reef monitoring programme in Jakarta Bay and the Seribu Islands has been initiated by the LIPI Research and Development Centre for Oceanology in collaboration with UNESCO. Through the collection of time series baseline data, the programme aims to study the dynamic changes of coral assemblages.

The first baseline data were collected in 1985 during an international workshop on 'Human-induced damage to coral reefs'. Twenty eight islands were surveyed and over 550 man-hours were spent collecting data on the islands' geomorphology and the biological status of the surrounding coral reefs. Coral growth, using the line intercept transect method (English et al., 1994) was measured along a pollution gradient from Jakarta Bay to the outermost part of the Seribu Islands, some 80 km from the coast. The results of the exercise showed that many of the reefs were in poor condition.

A second survey was conducted ten years later in 1995, during an international 'Coral reef evaluation workshop, Pulau Seribu'. This covered the same sampling sites and used the same methodology as the 1985 survey. A national 'Coral reef management workshop for Pulau Seribu', conducted in Jakarta and Pulau Ayer in 1996, provided a forum for different stakeholders – fishermen, scientists, teachers, journalists, NGOs, government officers and resort owners – to confront the problems. The workshop participants reviewed the research conducted in the 1995 survey of the Seribu Islands. The dramatically worsening status of the reefs caused much concern among participants and demonstrated the need for a more comprehensive response.

A dramatic decline in reef health in the Seribu Islands was recorded between 1985 and 1995 (De Vantier et al., 1998). The decline in coral cover and species richness may be attributed to outbreaks of crown-of-thorns starfish; temperature stress associated with the El Niño Southern Oscillation Phenomenon (ENSO) in periods in the 1980s (Suharsono, 1990) and possibly also in the 1990s (Harger, 1995); the spread of the sodium cyanide fishing technique in the 1990s; pollution from the Jakarta coastal area (Harger, 1986, Hungspreugs, 1988); and the muro-ami coral breakage in the 1980s and 1990s.

Table 1 compares coral reef cover between 1969 and 1995 for two of the Seribu Islands. Percentage cover was used as an indicator of coral reef condition, rather than species diversity, as this depends on other factors such as the density of reef colonies in the area. As can be seen there was a dramatic decrease over the period, especially between 1970 and 1985.

Location 1969–70 1985 1995
Pari Island 80% 22% 15%
Air Island 70% 25% 30%

Table 1.  
Percentage coral 
reef cover for two
Seribu Islands  

During the 1985–1995 assessments, the reef tract was divided into three groups based on oceanography, reef geomorphology and distance from the mainland. These groups were: reefs within Jakarta Bay, reefs of the mid-region (15–50 km offshore from Jakarta), and reefs of the outer region (> 50 km from Jakarta).

Reefs in Jakarta Bay remained in very poor condition in 1995, with little apparent change in coral cover since 1985. Living hard corals covered less than 5% of the substrate, and sand, rubble and algae were the dominant types of cover on most reefs. Water quality was very poor, with flotsam and high concentrations of plankton in the nutrient-enriched bay waters. Three of the nearshore islands had disappeared below sea level since 1985 and several others were eroding, probably through a combination of dredging for landfill and natural loss of sediments. High rates of bio-erosion were apparent on the inner region reefs, and there was little to no coral growth occurring to counter these effects. Thus, further erosion of the reefs and islands is likely, particularly if dredging continues. At present, most of these reefs can be considered functionally dead, mainly as a result of human impacts.

Reefs of the mid-region exhibited substantial variability in 1995, ranging in coral cover from less than 10% (Pulau Tidung) to more than 50% (Pulau Dapur). Since 1985, several reefs had increased in coral cover, others showed little change and one showed a major decline in cover (Pulau Tidung). Overall, coral cover remained at approximately 20% and had shown a slight increase. Although included in this mid-region, the reefs of Pulau Damar Kecil and Pulau Untung Jawa appear to represent the transition zone between the major influence of Jakarta and the adjacent mainland. Cover of living hard corals on these reefs was approximately 10% in 1985 and 1995. By contrast, coral cover had increased substantially on Pulau Damar Besar (by approximately 15 to 30%) and Pulau Dapur (by approximately 25 to 55%) over the same period. These two reefs are both less than 25 km from Jakarta, indicating that water quality at this distance is not inimical to coral growth and recovery. Indeed, Pulau Dapur showed the greatest improvement in coral cover of all reefs surveyed in 1995, and was the only reef that could be considered to be in good/excellent condition (in terms of coral cover) by international standards.

Most reefs of the outer region exhibited declines in coral cover since 1985, particularly in corals of the genus Acropora on the reef slopes (3 m depth). In 1985, the outer region had the highest cover of hard corals (approximately 30%), and there was an overall improvement in reef condition with increasing distance offshore from Jakarta (Brown, 1986; Harger, 1986; Moll and Suharsono, 1986). By 1995, there had been a significant decline in coral cover, to approximately 20%. Blast fishing was occurring at the time of the 1985 surveys (Harger, 1986), however, there was no evidence of blast fishing in 1995, although poison fishing with cyanide was reportedly occurring in the region (Djohani, 1994). Overall, there was a marked absence of large reef fishes and other fauna of commercial value (e.g. holothurian 'sea cucumbers') at most sites, and an increase in the abundance of sea urchins, particularly Diadema sp., and of crown-of-thorns starfish Acanthaster planci. These starfish appear to have been increasing in abundance in the Seribu Islands reef tract since 1985.

2.2.3. Other indicators of coral reef stress

In order to evaluate the potential of several new reef assessment techniques, the 1995 UNESCO-P30 LIPI survey of the Seribu Islands reefs was expanded in scope to include surveys of both stomatopod crustaceans and echinoderms. Stomatopod crustaceans are particularly well suited for inclusion in large-scale, rapid coral reef assessments for they are ubiquitous, abundant, and diverse in the Indo-Pacific region, and their populations are easily sampled objectively without the use of SCUBA equipment. As stomatopods are an important component of the abundant mobile cryptofauna of coral reefs, study of their populations can offer insight into reef processes which might otherwise be missed. Stomatopod abundance, diversity and recruitment are very negatively correlated with sediment concentrations of petroleum hydrocarbons and certain heavy metals, and with surrogate measures of sewage and agrochemical runoff contamination (Steger and Caldwell, 1993).

Despite some exceptions, the general trend of increasing stomatopod abundance with distance from Jakarta is pronounced. Detailed analyses proved that stomatopod abundance was highly correlated to a number of water quality parameters, many indicative of marine pollution.

In relation to stomatopod diversity the results show that the reefs in Jakarta Bay are exclusively dominated by two species (G. viridis and G. hendersoni). In the central region of the archipelago, species diversity rises from two to seven species, while in the northern part of the Seribu Islands species diversity drops to four.

This interesting pattern of highest species richness in the central zone of the archipelago has also been demonstrated for the hard coral (Moll and Suharsono, 1986; Brown et al., 1983). The process responsible for this pattern of species richness has not yet been fully explained. Moll and Suharsono (1986) consider that increasing human impact with proximity to the mainland may be of primary importance; this may account for the observed structuring of stomatopod communities as well. However, this theory fails to account for the slightly decreased species richness in the northern Seribu Islands reefs, which ostensibly suffer the least from human impacts. Brown et al., (1983) conclude that the lower coral species diversity on the northern reefs may be a result of increased exposure to high wave energy on those reefs. A synthesis of the observed pattern of species richness could result in a variant of the 'intermediate disturbance hypothesis', which holds that species diversity is often highest in areas where intermediate levels of disturbance act to 'maintain local diversity by preventing the elimination of inferior competitors' (Connell, 1978; Karlson and Hurd, 1993). Jakarta Bay reefs seem strongly affected by human disturbances such as marine pollution, dredging and sedimentation, so that only pollution and sediment-tolerant species are able to exist in these zones. Likewise, the northern Seribu Islands reefs may be strongly affected by wave exposure, which also limits species richness by excluding exposure-intolerant species. The central zone of the reef is affected by both human impacts and physical exposures, but only at 'moderate' levels. This situation may allow a larger number of species to coexist on the central Seribu Islands reefs.


There are many factors involved in ecosystem degradation in Jakarta Bay, some of them natural such as the high sea surface temperatures during the El Niño episodes, many others are man-induced. This section will discuss several of these causes, namely: the bleaching event in 1998; sand and coral extraction and mangrove clearance; destructive fishing practices; and pollution.

2.3.1. Bleaching event in 1998

Extensive coral bleaching was observed in Indonesian waters in 1998, from Riau Islands (East Sumatera) to the Seribu Islands (off Jakarta), Karimunjawa Islands (Central Java), Bali and Lombok Islands. In the islands of Bali and Lombok, the first signs of bleaching were reported in early March 1998, while in the Seribu Islands they were only observed in early May 1998. By the end of June 1998 extensive mortality was noted. About 90-95% of the corals extending from reefs flat down to a depth of 25 m were affected. Acropora spp. were the most impacted species. Regular monitoring of sea surface temperature at Pari Island (Seribu Islands) revealed that a warming occurrence began on 10 January with a maximum around 19 March 1998. The average daily sea surface temperature at Pari Island was 2–3ºC above normal values. The satellite data showed that warming water originated in the Gulf of China in August 1997 and travelled to the South China Sea, Malaysia and Singapore, as well as to Riau Islands and the Java Sea. The warming water also originated off western Australia flowing through the Timor Sea and the Indian Ocean.

2.3.2. Sand and coral extraction and mangrove clearance

Large scale sand extraction started with harbour dredging in the Jakarta Bay area, generally the dredged material was dumped elsewhere in the bay. In the 1970s, sand extraction for building started on a small scale and was carried out manually. Since the 1980s, extraction has intensified and is now of great economic importance to various small communities along the coast.

Hardenberg (1939) reported that coral harvesting in the Seribu Islands reefs started in the early part of the twentieth century. He estimated that 12,000–25,000 m3of coral reef cover were exploited annually. Verwey (1931) estimated the annual removal of coral reef in the 1930s at 8,500–20,000 m3 in the Seribu Islands. Nowadays, it is estimated that the scale of exploitation has escalated significantly, based on a doubling of quantities between 1979 and 1982.

Extensive dredging activities have been allowed to proceed, despite local government regulations banning the exploitation of sand, gravel and boulders, in order to provide construction materials.

In addition, mangrove destruction for land reclamation for residential and fishpond development has resulted in increased sedimentation, loss of species habitat and ecosystem degradation.

2.3.3. Destructive fishing practices

Over-fishing, as well as the use of destructive fishing practices, such as blast and cyanide fishing, have resulted in a decline in fish catches.

At present hundreds of fishing boats, either motorised or sail-powered, operate in the waters of the Seribu Islands everyday. Boats powered by 5–75 horsepower outboard motors are most commonly used, but some fishers still use sailboats. The boats are not always their own property. The fishing industry 'hierarchy' consists of 'bosses' (boat owners), boat captains and crew.

Fishers in the Seribu Islands can be classified into two groups: those catching fish for human consumption (larger fish such as snapper, oil sardine, yellow tail and mackerel) and those catching ornamental fish. The principal fishing equipment is fishing rods and plaited rattan fish traps.  


Traditional fishers, like those in the Seribu Islands, are very dependent on the weather and usually only fish six to ten months of the year. There is a period, usually between November and March, when the sea is often rough. During these non-fishing months people have to live off their savings and they are far from financially secure. In order to alleviate this problem, they sometimes risk fishing in the calmer periods of the bad months.

Fishers in the Seribu Islands only fish in local waters. However, since the region was designated as a marine national park, fishing grounds have been limited. Consequently their income has decreased. Some fishers now fish outside their home area, in the waters of Lampung Province, Bangka and around the Sunda Straits. Many fishers think that if they do not take the resources, others will. Consequently they use the technology which enables them to make the biggest catch possible, e.g. blast fishing and cyanide fishing.

Blast fishing, using explosives to stun or kill fish, kills indiscriminately both targeted and non-targeted fish, as well as invertebrates of all but the largest classes. It also damages or destroys the reef framework. Repeated blasting can result in reefs that are little more than fields of rubble punctuated by an occasional massive coral head. Although blast fishing is illegal in Indonesia, it is still quite common throughout the archipelago, particularly on remote reefs where the threat of law enforcement is low. Erdmann (1998) reported that blast fishing was one of the most widespread and devastating of fishing practices in 1985, but it was neither observed nor heard of during the 1995 survey. Blast fishing works best on dense schools of fish, now an uncommon sight in the Seribu Islands. The disappearance of blast fishing may be related to an absence of target fishes.

The use of sodium cyanide to stun fish for live collection is a widespread activity in the Seribu Islands. As with blast fishing, it is often indiscriminate and large side-kills of larval and juvenile fish, as well as invertebrates, are common. Prior to 1990, the principal targets of cyanide fishing were ornamental fish and invertebrates in the aquarium trade. In the years following 1990, a new lucrative cyanide fishing trade infiltrated Indonesia: the live reef fish food trade. Several groups of fish are targeted for live collection and eventual export to wholesalers for consumption primarily abroad.

Making destructive fishing practices illegal has not been sufficient to halt the activities, economically they are too rewarding.

2.3.4. Pollution

The hinterland is the primary source of pollution in Jakarta Bay. All the wastewater from the Jakarta Metropolitan Area ends up in Jakarta Bay. Several major coastal rivers transporting sediments, sewage, agricultural and industrial effluents, and solid waste flow into Jakarta Bay. This has resulted in high nutrient levels and eutrophication of coastal waters extending over a considerable distance – as far as the Java Sea.  

Poverty and 
in one of the 
rivers that 
drain Jakarta


A review of historical data indicates that Jakarta Bay is becoming progressively more eutrophic. Nutrient concentrations have increased in Jakarta Bay and the Seribu Islands since 1969. High nutrient concentrations have been identified as the main cause of increased primary productivity in the surface waters. Chlorophyll a concentrations measured in Jakarta Bay by Nontji (1978) ranged from 5.41 to 12.3 mg/m3; suspended particulate matter concentrations were between 10 and 79.6 mg/l in 1975 and 1976. Praseno and Adnan (1978) documented massive diatom blooms.

Phytoplankton biomass distributions in Jakarta Bay, measured from 1986 to 1990, have undergone significant shifts; phytoplankton blooms are now spreading further offshore. In 1986 massive algal blooms were detected as far as 2 km from Jakarta's port, Tanjung Priok. However, in 1988 the blooms spread 5 km offshore and in 1990 massive algal concentrations were recorded 12 km from the port.

There are three major sources of pollution: industrial, domestic and agricultural activities. Two types of industrial pollutants have been identified in Jakarta Bay : heavy metals and polychlorobiphenyls (PCBs). Jakarta's Office of Urban Environmental Study reported in 1997 that the heavy metal content (copper, lead and mercury) in Jakarta Bay waters had been increasing since 1983. Hutagalung (1987) and Mahbub and Kuslan (1997) showed that this pollution is a result of industrial waste. PCBs are used in dielectric fluid for capacitors, transformers, the production of carbon-free copy paper and the manufacture of ink; they are non-biodegradable, lipophilic and carcinogenic. Razak (1994) reported that PCBs can be found in marine plankton, fish, mammals, birds and the human body. Marine activities, including ship waste, oil spillage and offshore mining are other sources of industrial pollution.

The rivers flowing through the Jakarta Metropolitan Area pick up large amounts of domestic effluents and solid waste. Since there is no sewage treatment, these rivers are heavily polluted with organic nutrients and bacteria. In addition, the water drainage system in the Jakarta Metropolitan Area is degraded. A third of northern Jakarta is flooded on average twice a year. This situation, which seriously affects 5% of the city, is exacerbated in some areas by subsidence.  

in Kapuk


Razak and Khozanah (1994) reported on the pesticide content in Jakarta Bay waters and sediment, based on observations made in September and November 1993. The persistent pesticides and derivatives detected were dieldrin, aldrin, heptaclor and endosulfan. Erosion caused by agricultural activity constitutes another source of pollution – suspended sediments in rivers and Jakarta Bay waters. Land reclamation is another cause of increased suspended sediment.

A serious 
adds to 
river pollution


Solid waste, which may originate from domestic, industrial or agricultural sources has increased since 1985. During the 1985 workshop on 'Human-induced damage to coral reefs', strand-line pollution was measured on 24 islands in the Seribu Islands. The survey was repeated in 1995 on 18 islands. Total shoreline litter increased about two-fold between the two surveys. This is reinforced by data on the maximum amount of litter found on a single transect. In 1985, more than 1,000 items of litter were found on a 50 m transect; in 1995 nearly 2,500 items per 50 m were found on Kelor and more than 1,000 per 50 m were found on eight occasions in six other islands: Damar Kecil, Onrust, Bidadari, Untung Jawa, Rambut and Bokor. Evidence points to Jakarta as the source of much of this litter.  

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