A study of nutrients, underwater light dynamics, and their correlation with phytoplankton biomass was conducted in the tropical estuary of Jakarta Bay, Indonesia, in the dry season during the period from 2001 to 2019. This study analyzed the spatial and temporal dynamics of phytoplankton biomass and its correlation with phytoplankton biomass. There was significant increase in nutrient concentration in Jakarta Bay, with annual means of 27.97 µM dissolved inorganic nitrogen (DIN) and 11.31 µM phosphates in 2001, increasing to 88.99 µM DIN and 25.92 µM phosphates in 2019. Increased mean nutrient concentrations were accompanied by increased mean phytoplankton biomass, from 15.81 µg Chl-a L⁻¹ in 2001 to 21.31 µg Chl-a L⁻¹ in 2019. The eutrophication status of Jakarta Bay waters was calculated using the Tropical Index for Marine Systems eutrophication index, which showed increased areas of hyper-eutrophic and eutrophic zones, while the mesotrophic area decreased. The hyper-eutrophic zone dominated the areas around river mouths and the inner part of the bay, while eutrophic status was observed in the middle part of the bay and mesotrophic status was found in the outer part of the bay. The area of hyper-eutrophic water increased 1.5-fold, from 75.1 km² in 2001 to 114.0 km² in 2019. Increasing eutrophication of the bay has had negative ecological consequences including algal blooms, hypoxic conditions, and mass mortality of marine biota, and it urgently requires remediation.

In this study, the composition and distribution of phytoplankton pigments and its relation to nutrients and light was investigated, and an elaboration of using it as a proxy for phytoplankton group composition followed, in different nutrient-level tropical bays of Indonesia. Phytoplankton pigment analysis by using High Performance Liquid Chromatographer (HPLC) resulted in a set of pigments of chlorophyll-a (Chl-a), chlorophyll-b (Chl-b), chlorophyll-c (Chl-c), lutein, zeaxanthin, fucoxanthin, peridinin, diadinoxanthin, and ß-carotene. Linear multi regression and multivariate principal component analysis (PCA) showed that algae pigments correlate positively with nutrients and are not significantly correlated with underwater light and water transparency, suggesting important roles of nutrients for phytoplankton development in tropical estuaries. There were differences in total algae pigment concentration between bays (p < 0.005), showing that the eutrophic system of Jakarta Bay was the highest (mean of 10.55 μg L⁻¹), Lampung Bay was the second highest (mean of 3.37 μg L⁻¹), and the lowest were the oligotrophic waters of Semangka Bay (mean of 0.80 μg L⁻¹). At all bays studied, high nutrient sites, which were located in the river mouths and inner part of the bay, were always characterized by high phytoplankton pigment concentration. Pigment composition had a high correlation with phytoplankton composition: diatoms with fucoxanthin, dinoflagellates with peridinin and Chl-c, and Chlorophyceae with Chl-b and lutein. This conformity suggests that algae pigments can be used as a biomarker for phytoplankton group determination along with microscopic species identification.

An integrated institutional approach is expected to be a solution to overcome this policy fragmentation. With integrated mangrove management across jurisdictions, it can be clearer to maintain the sustainability of the mangrove ecosystem while supporting sustainable development in the coastal area of Jakarta Bay. This study aims to develop an ideal inter-jurisdictional institutional framework for mangrove management in Jakarta Bay. The study used primary and secondary data. Data analysis uses stakeholder analysis, multidimensional scaling (MDS), and interpretive structural modeling (ISM). The results of the stakeholder classification showed that local communities occupy the subject category, the key players are the central government and regional governments, universities and NGOs occupy the context setter position, and the crowded category is the private sector. The results of the MDS analysis using RAP Mangrove show a sustainability index value for the institutional dimension of 11.59%. The institutional design of the three elements, which are divided into 11 sub-elements, shows that the availability of adequate data and planning for the implementation of mangrove rehabilitation, restoring mangrove ecosystems in damaged conditions, improving the quality of degraded mangrove cover and ponds, and mangrove rehabilitation at the multi-strata government policy and program level (multi-related sectors, regional government, and village government) are the basis for the achievement of the other sub-elements. Synchronization of regulations and policies across sectors, as well as active participation from various stakeholders, are the keys to success in maintaining the sustainability of mangrove ecosystems.

The accumulation of plastics in marine environment has increased the global risk of water pollution. Its uncontrolled production and existing management capacity have brought a burden on current plastic waste management, especially in Jakarta Bay. It has a negative impact on land, ecosystems, and especially the food chain and marine organisms. Their improper management has reduced the quality of environment, human health, and influenced economic sectors. Economic activities which involve coastal areas have consistently become a major source of plastic waste leakage either directly or indirectly. This study aims to analyze current source and its distribution patterns of plastic waste leakage in estuaries of Jakarta Bay using in-depth interviews and field observations. The results show the estuaries at the eastern part of Jakarta Bay is the highest potential for plastic waste leakage, followed by the western part, and the middle part is the least contributing plastic waste of leakage. The various sources of leakage in the estuaries are identified, including the behavior of the community that is vulnerable to exacerbates the existence of leakage. Handling capacities are limited including facilities, and the intensity of collection in the wide coverage of the operating area made the challenges to the responsible authorities.