Indonesia, as a tropical region, has an incredibly high aquatic biodiversity. Organisms are distributed throughout various aquatic ecosystems such as rivers, lakes, ponds, estuaries, mangroves, seagrass beds, and coral reefs. These ecosystems have immense potential in supporting fishery production. However, in utilizing these resources, human activities are often uncontrolled or environmentally unfriendly, such as coral mining, fishing with explosives and/or toxic substances, the use of production tools like fertilizers and pesticides in agricultural or aquaculture activities, and other activities in coastal and/or marine waters. These activities not only impact the sustainability of marine resource ecosystems in coastal areas, such as estuaries, mangroves, seagrass beds, and coral reefs, but also those in upstream areas, such as watersheds, lakes, or reservoirs. Therefore, to preserve the potential natural resources in these ecosystems, the following sections will provide a selective overview of how to manage the potential aquatic biological resources.