The Prince of Wales has been forced to adapt his latest plans to expand his ‘sustainable town’ because of fears over river pollution.

Prince Charles wants to build 1,200 new houses as well as a primary school and more shops in Poundbury, near Dorchester in Dorset.

But Natural England feared that the extra sewage effluent going into the River Frome could harm birds and wildlife.

Charles has now agreed to cut river pollution from Duchy Farms alongside the threatened river as a condition of building hundreds more homes at the new town.

There were fears that effluent from the farm’s treated sewage would upset the ecosytem of the River Frome, whose rich fauna includes salmon and water voles.

The river is exceptionally low at the moment, although the drought which has struck south east England has not hit the West Country.

Any future drought would leave the river vulnerable to inevitably high concentrations of pollution.

Nitrates feed algae and high levels can produce massive algal “blooms” which can kill fish and other water life by reducing oxygen levels.

The Duchy of Cornwall estate wants to build 1,200 new houses, a primary school and shops in an expansion which should complete his urban extension of Dorchester.

Poundbury was begun in 1994, already has around 1,000 homes, and is said to have boosted the local economy by £331 million. The Prince, renowned for his concern for sustainability and conservation, reached an agreement with Natural England on the pollution issue.

Dr Phil Sterling, ecological adviser to West Dorset District Council, said the high levels of nitrates in the the Frome has caused a huge algal mat to grow in Poole Harbour, covering protected mud flats and making it impossible for rare wading birds to feed.

He was confident the deal with the Duchy could reduce nitrate flows so that the houses could be built.

“We want to get to a position where we can see a more sustainable outcome, so whether there is a drought or not, it does not effect the quality of the water for wildlife or the water we are drinking.”

Miles King, director of conservation for the Grasslands Trust, said Prince Charles’ action could inspire other farmers to cut down on artificial fertilisers by going organic or using new technologies. such as computers on tractors to ensure fertiliser is only spread on areas of the field where it is needed. Environmental measures such as reed beds in ditches, grazing less cattle and digging ponds can also help.

“This is an example of how we can manage the countryside because we all need the services it provides,” he said.

A Duchy spokesman said: “As part of the planning approval for the next phases of Poundbury, the Duchy has agreed with Natural England a strategy for reducing nitrate levels on its land in the Frome catchment area by encouraging its tenants to use organic farming methods.”

“This is one of a number of options considered, and is very much in line with the Duchy’s land management principles and those of HRH The Prince of Wales.

“No timelines have been set at this time, although we would anticipate a change in the farming practices to take over the next few years.”