In four of the past 10 years, Environment Canterbury has described Lake Georgina in the upper Rakaia high country as "green and murky with higher amounts of nutrients and algae". Most of the 14 lakes ECan measures have become murkier over this time.

Canterbury high country lakes once rated "clean and blue" are being fouled by nutrients and phosphorous from intensified farming.

The purity of lakes from Lake Coleridge to the Rangitata River, including Lakes Selfe, Grasmere, Hawdon, Alexandrina and Ida has declined in the past 10 years, Environment Canterbury (ECan) monitoring shows.

On an ECan rating of 1 to 6, lakes that had been "clear and blue" are now mostly in "moderate" condition with nutrients and algae present.

ECan has been working with high country farmers on ways to control the amount of nitrogen and phosphorous seeping into alpine waterways.

It is these nutrients that feed plant growth in the lakes, changing the clarity, colour and ecosystems in them.

ECan classes "nutrient loading" as a major threat to the condition of 25 lakes, in the upper Rakaia Gorge, Ashburton Basin and along the upper Rangitata.

Water consultancy the Cawthron Institute last year reported to ECan and Department of Conservation on nutrient loading in the high country.

Changes in farming to more intensive practices, including grazing for the dairy industry, and growing crops for livestock created a risk of more nutrient going into lakes.

ECan had classified 25 lakes on its watch into "sensitive lake zone catchments".

A pilot study around the Ashburton lakes showed the shallowest were the most vulnerable to "further degradation", either from farming or pollution from bird droppings.

The Cawthron study said low-intensity sheep and beef farming was giving way to dairy support and crops like fodder beet. Irrigation usually made this possible.

At the time of the report, a number of properties in parts of inland Canterbury were seeking resource consents for dairying. These changes, which extended to areas like the upper Waitaki basin, would "almost certainly result in an increase in nutrient run-off".

The potential effects of this on freshwater environments were poorly understood, Cawthron said.

Federated Farmers senior policy analyst Lionel Hume said farm environment plans helped farmers to match their use of nutrients, like fertiliser, to what the land really needed. The plans would also help farmers to irrigate more efficiently and minimise runoff from drainage, for example.

Farmers in the sensitive lakes zone would be given a nitrogen discharge baseline, which could prevent them farming more intensively. That could mean fewer sheep or cattle, different crops or less irrigation for pasture.

Hume said some of these nutrient limits could be a stumbling block block in tenure review, the Crown's negotiations for freeholding leasehold land.

A farm-owner planning land swaps with the Department of Conservation or other agencies under tenure review could get a shock from being unable to intensify their new freehold, he said.

ECan surface water science manager Tim Davie said the clarity of small high country lakes like Lake Georgina in the upper Rakaia area could be greatly affected by a warm summer while deeper lakes like nearby Lake Selfe was more stable.

Lake Selfe had a small decline on ECan's Trophic Level Index (TLI) but the change had not been particularly large since 2008, he said. A lake that shown significant improvement in TLI was Lake Emma in the Ashburton Lakes region. It had "responded to significant effort fencing off the surrounding wetland", Davie said.

High country farmers in the sensitive lake zones are well on the way to completing their environment plans, an ECan land management officer told the Selwyn Waihora water zone committee last week.