Environmental threats to marine ecosystems have traditionally been associated with the influx of pollutants from land and the atmosphere as well as from human activities at sea. However, many threats have been identified nowadays that result from other causes. Among other things, the seabed can be an internal source of pollution for the ecosystem, either largely related to anthropogenic pressure. On the seabed, there are dumped chemical and conventional munitions, wrecks, and sunken hazardous materials. This is partly due to hostilities and maritime disasters, but also the deliberate dumping of waste. Additionally, historic emissions of pollutants have led to seabed contamination in some areas. Continuous biogeochemical processes occurring in the top layer of sediments may lead to a negative impact on the ecosystem, e.g. by increasing the bioavailability of metals, excessive oxygen consumption and release of these pollutants into the water column, what can significantly affect the benthic and pelagic habitats. Another threat not related directly to the inflow from the mainland is the accumulation of biomass in coastal areas and its decomposition on the beach and in the surf zone. During this process, the contaminants accumulated earlier from the water column and sediments are released back to the environment. The accompanying high concentrations of organic matter and bacterial activity can lead to increased concentrations of toxic substances and their higher bioavailability in the coastal zone. Other intra-system threats to the marine environment are also economic activities in the marine environment, such as the construction of pipelines, wind farms, or other structures as well as the effect of climate change on the circulation of elements, their remobilization, and bioavailability.