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Environmental problems can increase due to anthropogenic activities or natural phenomena. Indonesia is an archipelagic country that consists of many islands and coastal regions, where the growth of anthrophogenic and natural activities has exhibited severe environmental degradation in the past few decades. The collection of baseline data from all sectors of the environmental sectors is important to avoid any impact before a real action is made. Hydrocarbons such as aliphatics (n-alkanes) and polycyclic aromatic hydrocarbons (PAHs) are widespread contaminants throughout the environment that mainly originate from the combustion of fossil fuels, biogenic and terrestrial sources (antrophogenic), along with the direct release of oil and oil products (petrogenic sources). In addition, the Stockholm Convention is a global environment agreement developed by the support of UNEP (The United Nations Environment Programme) that was signed on May 23, 2001. The aims of the Convention are to protect human health and environment from the adverse impact of POPs (persistent organic pollutants). Indonesia has signed the Convention and is in a process for ratification, one of the requirements being a National Implementation Plan to manage the utilization of POPs in Indonesia. Persistent organic pollutants such as polychlorinatedbiphenyls (PCBs) and organochlorin pesticides (OCPs) are hydrophobic, liphophilic, ubiquitous compounds with bioaccumulable behaviour that are banned globally under the Stockholm Convention on POPs. This study aims to explore (both qualitatively and quantitatively) the extent and sources of organic contaminants, i.e. n-alkanes in surface sediments; PAHs, PCBs and OCPs in sediments and mussels, P. viridis from Jakarta Bay, North Jakarta, Indonesia, using ratios or indices selected to diagnostic compounds and P. erosa from the Segara Anakan Lagoon. Analysis of hydrocarbons has been conducted with soxhterm extraction and adsorption chromatography as purification methods. In addition, PCBs and OCPs have been conducted with accelerated solvent extraction (ASE) combined with alumina as purification methods. Furthermore, the analysis of PAHs, PCBs, and OCPs in the mussels were done using QuEChERS (Quick, Express, Cheap, Robustness) with extraction and solid phase extraction as purification methods. Each protocol was continued with qualitative and quantitative analysis by GCQQQ(triple-quadropole)/MS. The sum of 16 PAH contents in surface sediments ranged from 187µg.kg-1to 916µg.kg-1 sediment dry weight (dw); meanwhile, the sum of seven PCB contents ranged from 3 to 117µg.kg-1dw and the sum of OCPs contents ranged from 3 to 17.99µg.kg-1dw. For mussels, P. viridis, the sum of 16 PAH contents ranged from 591µg.kg-1 to 997µg.kg-1 mussels dw and OC contents ranged from 5 to 6µg.kg1mussels dw. ?7PCB concentrations in sediments were found in the range of 0.11±0.05 to 2.63±0.1?g.kg-1sed. dw, and OC levels were found in the range of 0.2±0.05 to 2.9±0.01?g.kg-1 sed. dw. Sixteen polyaromatic hydrocarbons (PAHs) (USEPA) in P. erosa were analyzed and found in the range of 103.34±2.01 to 1348.31±18.21µg.kg-1 tissue dry weight (dw); the OC contents were found in the range of 0.87±0.03 to 24.79±1.30µg.kg-1 tissue dw. Those experiments were done with repetition except for n-alkanes and PAHs in sediment from Jakarta Bay. Matric interferences have been evaluated with proper samples and suitable yields of extraction and analysis. Several ratios of selected PAHs anthracene/?178, fluoranthene/?202, benzo(a)anthracene/?228, and indeno(1,2,3cdi)perylene/?276 showed that the sources of hydrocarbons in the sediments and mussels were generally biogenic, including both terrigenous and marine, with an anthropogenic pyrolytic contribution (petrogenic and biogenic combustion). Environmental risk assessment parameters such as Treshold Effect Level (TEL), Effect Range Median (ERM), and Effect Range Low (ERL) from sediment quality guidelines (SQGs) were used to evaluate the probability risk in marine environments. Besides SQGs, sediments and mussels also in regard to the extent of the PAHs, PCBs, and OCPs (i.e. pp’-DDE) have been compared to other studies conducted at some polluted sites. AFSSA (French Agents of Food Safety) recommended dosage PAH based on US-EPA (United States-Envrionmental Protection Agency) to evaluate the biota (P.viridis and P.erosa) in terms of food security. Those data can serve as a baseline reference for the future assessment as part of the integrated watershed management program involving biodiversity, fresh water ecology, and economic activity in the area of this study. If such information is not available a future assessment regarding the environmental impact of anthropogenic activities will be more difficult and less accurate.