Mangrove forests support the global ecosystem and serve as blue carbon reservoirs. However, they are facing threats from climate change phenomena, such as sea level rise, and human activities, such as deforestation, erosion, pollution, reservoir construction, and coastal development. Few studies have examined the trends regarding carbon, nutrients, and pollutants in mangrove systems due to climate change and human activities over a timescale of 100–150 years. Thus, in this study, sediment cores were collected from the coastal fringes of mangrove forests across East and Southeast Asia to evaluate total organic carbon, total nitrogen, sediment phosphorus species, and microplastics. Our results showed that the differences in the spatial and vertical distribution of sedimentary organic matter, carbon stock, phosphorus species, and microplastic were attributable to various factors such as tree age, geomorphic settings, sediment characteristics such as particle size, organic matter, and nutrient contents, and physical influence such as tidal effect and the intensity of human activities. The results of this study will provide important information for policymakers to use in maintaining the sustainability of these fragile ecosystems.