Higher temperatures and rising sea levels have changed the nature of many of the fundamental problems faced by marine conservationists, said Barbara Young, the agency's chief executive. "The good news is that major historical issues such as sewage pollution are being addressed and their impact reduced," Baroness Young said.
"Sadly, other impacts, such as climate change, are becoming an increasing threat to the marine environment and those that depend on it.
The Environment Agency's latest review of the marine environment found that coastal erosion, flooding and the effect of climate change on marine wildlife had increased the long-term risk to the British coastline. "Climate change is significantly altering the marine environment and affecting populations of marine life," the study says
Average sea-surface temperatures around Britain have increased by between 0.5C and 1C over the past century, which has driven microscopic marine plants called phytoplankton further north. "Warmer temperatures since the late 1980s have encouraged higher phytoplankton densities that have made our seas greener in colour," the report says.
Changes in phytoplankton have also altered zooplankton, microscopic animals on which many fish such as cod feed. "This has contributed to falling cod populations. Cod and other species of fish are also moving north," the report says.
Over the past 40 years, warmer seas have forced many marine animals and plants to move roughly the length of Britain toward the cooler seas of Scandinavia.
Sea levels are increasing by about a millimetre per year and the level of the highest tides and the average height of winter waves have increased. As a result, coastal erosion has increased, with 6 per cent of sites in England and Wales and 20 per cent of sites on the east coast eroding at more than a metre every year.
"The erosion of our coasts is likely to increase with climate change, with the cost of damage from erosion estimated at £100m a year," the report found.
The Environment Agency estimates that climate change could increase by between four and tenfold the risk of flooding unless more money is spent on reinforcing coastal defences.
Despite improvements in pollution controls, about 80 per cent of marine pollutants still come from the land and a quarter of Britain's coastal waters are at risk of "diffuse" pollution caused by inadvertent run-off of farm fertilisers and pesticides.
Fish stocks have fallen to historically low levels with only 38 per cent of fish in UK waters being harvested sustainably, the agency found.
Sir John Harman, chairman of the Environment Agency said that Britain needed to strike a better balance between the different use of our coasts and seas to protect the marine environment. He said: "Already animals such as the basking shark which rely on small sea organisms for food have migrated north. A survey of UK coastal waters found 172 of 187 basking sharks were in Scottish waters."
The Environment Agency said there were still many unknowns about Britain's marine ecosystem that could affect its long-term health.
"The marine environment is under threat, [but] the nature and extent of these threats are often unclear," it said.