Monitoring has revealed that phosphate levels at the SSSI are three times higher than they should be.
These levels are causing biological harm and producing algae and duckweed, which is harmful to wildlife.
A release from NE and the Environment Agency (EA) said that the primary sources of phosphates are agricultural activities and water industry discharges from waste water treatment works and sewer overflows.
NE says it will now work with Wessex Water, the EA, landowners, farmers, and wider stakeholders, to put solutions in place.
This will include further investment by Wessex Water of up to £57m to reduce discharge from water treatment works by 2024, according to the nature regulator.
NE also says there will be regulatory enforcement and advisory visits to improve agricultural compliance and provide advice to farmers and landowners, as well as unspecified new solutions which will allow landowners to be appropriately rewarded for the ecosystem services they provide.
Jim Flory, environment manager for EA Wessex, said they would be continuing to focus “available resource” on working with partner agencies and local authorities to drive improvements to protect the site.
He added: “One of the key actions is for us to undertake regular enforcement and advisory visits to improve agricultural compliance and provide advice to farmers and landowners”.
In March, at an Environmental Audit Committee inquiry into water quality in rivers, Dr Rob Collins, head of policy and science at the Rivers Trust said: "We've seen something like a 50% decline in [EA] funding for enforcement activities, the agency undertakes something like 50% less water quality sampling as it used to. They really are under-resourced for this".
Matt Heard, NE area manager for Wessex, said “there is widespread evidence that nutrient pollution is causing biological harm in the waterways of the Levels.
“Natural England is working with partners to deliver action that will restore water quality, aid nature’s recovery and improve the natural environment for local people and visitors to enjoy”.
Alarms had been raised earlier this year when Natural England published guidance over unacceptable amounts of phosphates in the Somerset Levels and Moors Ramsar site.
The guidance stipulated that local authorities should undertake a Habitats Regulations Assessment (HRA) before determining applications that may give rise to additional phosphates.
This led to Somerset’s four district councils and the area's county council publishing a phosphates calculator in a bid “to minimise delay and uncertainty around planning applications” caused by Natural England’s advice.
The leaders of Somerset West and Taunton, Sedgemoor, Mendip and South Somerset district councils also sent a joint letter to the government stating that the requirement to demonstrate that proposed developments will be phosphate neutral had so far led to the determination of hundreds of live planning applications in Somerset being halted, including those that would deliver over 11,000 new homes.