Of 62 sites around the region where water quality is tested every two months, 33 sites showed "meaningful declining water quality" trends during the past decade, the council's state of the environment report on surface water quality found.
Water quality scientist Rachel Ozanne said in a report to the council's natural resources committee to be considered tomorrow the report re-confirmed areas within Otago where land use was putting pressure on waterway health.
The sites with a trend of degrading water quality over the longer term tended to be smaller streams in agriculturally intensive catchments, she said.
"The trend analysis had identified that some of these rapidly intensifying catchments have increasing nutrient levels, particularly the Kakanui River catchment, Shag River, Catlins River and mid-Taieri."
In the shorter term, 18 rivers showed a trend of declining water quality - nine in the Clutha catchment, four in the Taieri and five in coastal catchments, with the Heriot Burn in the Pomahaka, Manuherikia at Ophir and the Waipori River showing high levels of nutrients or E coli in two categories. Lakes Waihola and Tuakitoto also had meaningful declining trends.
The monitoring measured levels of dissolved reactive phosphorus, nitrogen, E. coli, turbidity and dissolved oxygen in the waterways. The levels were then assessed against national water quality guidelines.
Of the 62 sites monitored for the 2006-11 report, 36 were classified under the water quality index as very good, 10 were good, 12 were fair and four were poor.
"The [water quality index] identifies many rivers as having very good water quality. However, many of these catchments have undergone recent change to more intensive farming."
Those rivers with poor water quality were in Southwest Otago (8) and around Dunedin (3), where small streams drained developed land and as a result had elevated bacteria and nutrient levels, she said.
Excellent water quality was found in catchments dominated by tussock, mostly the upper catchments of large rivers, outlets from large lakes and lesser developed areas of Otago, she said.
When the classifications were compared with 2001-06 data, 38 sites' water quality stayed the same, 10 recorded degraded readings and 13 showed an improvement.
Of the 10 which experienced a drop in water quality, Lake Tuakitoto, near Kaitangata, and Waipahi at the Cairn near Clinton in South Otago dropped two grades as some nutrient levels doubled.
The council was proposing changes to its water plan to improve water quality in the region and when the water quality index figures were compared with the proposed guideline values in water plan change 6A, 46 sites retained their traditional grading, eight dropped one grade and three dropped by two - Mill Creek, Silver Stream and Waianakarua River, Ms Ozanne said.
Four sites increased by one grade - Catlins River, Kaikorai Stream, Water of Leith and the Waipahi River.
After the 2007 state of the environment report, the council developed studies of the Pomahaka, Catlins and Manuherikia catchments to gain a better understanding of the problems, she said.
A study on the upper Taieri is about to be completed and studies are planned for the Kakanui, Shag and Lake Tuakitoto catchments in 2012-13.
State of Otago's rivers
Otago region land area: 32,000sq km.
Largest catchment: Clutha River, 21,000sq km.
Second largest: Taieri River, 5060sq km.
Best water quality: Upper catchments of larger rivers and outlets from large lakes.
Worst water quality: Small, low level streams draining pastoral or farming catchments.
Intensive land use impacting on "good" water quality areas.
