Marine pollution is the harmful effect caused by the entry into the ocean of chemicals or particles. An associated problem is that many potentially toxic chemical's adhere to tiny particles which are then taken up by plankton and benthos animals, most of which are either deposit or filter feeders, concentrating upward within ocean foodchains. Also, because most animal feeds contain high fish meal and fish oil content, toxins can be found a few weeks later in commonly consumed food items derived from livestock and animal husbandry such as meat, eggs, milk, butter and margarine.

One common path of entry by contaminants to the sea are rivers. The Hudson in New York State and the Raritan in New Jersey, which empty at the northern and southern ends of Staten Island, are a source of mercury contamination of zooplankton (copepods) in the open ocean. The highest concentration in the filter-feeding copepods is not at the mouths of these rivers but 70 miles south, nearer Atlantic City, because water flows close to the coast. It takes a few days before toxins are taken up by the plankton .

Many particles combine chemically in a manner highly depletive of oxygen, causing estuaries to become anoxic.