Three sites have had alert/amber warnings at certain times since the summer round of testing began at the beginning of December, but readings for those sites at other times and for all other sites have been considered safe for swimming.
This summer the Kakanui River at Clifton Falls Bridge is the only site to have its most recent reading in the amber/alert range, recording 510 parts of E. coli per 100ml of water on December 28.
ORC duty director Scott MacLean said there was a large colony of nesting gulls at the site, in rugged terrain, about 5km above the Clifton Falls bridge.
"Unfortunately, these nesting gull colonies are likely to continue to cause high E. coli concentrations in the upper Kakanui River, particularly during the breeding season."
Other amber readings were recorded in the Taieri River at Outram on December 12 and 19, and in the Taieri River at Waipiata on December 15.
Mr MacLean said the Outram spikes were caused by high river flows on December 12 and heavy localised rainfall on December 19, and the Waipiata spike was caused by rising flows at the time of sampling, due to rainfall on December 12.
Readings at both sites had since fallen to the green band of fewer than 260 E. coli parts per 100ml of water, which was considered very safe for swimming, Mr MacLean said.
He said water quality in Otago’s rivers and at beaches was "generally pretty good over the summer", especially in the Central Otago and Queenstown Lakes districts.
"However, in poor weather, heavy rain flushes contaminants from urban and rural land into waterways and because of this we advise people not to swim for at least two days after heavy or prolonged rain — even if a site generally has good water quality."
Several other sites have had only green readings since the beginning of December, but still have a general caution.
The advisory — on the Land Air Water Aotearoa (Lawa) website, accessed through the ORC website — for the Kakanui Estuary says at times that site can be high risk, with a 10% or greater risk of illness; Waikouaiti at Bucklands is at times high risk, with a 5% or greater risk of illness; Otago Harbour at Macandrew Bay, and Brighton Beach at Otokia Creek have a 5-10% chance of illness; and the Manuherikia River, at the Shaky Bridge, in Alexandra, has a 1-5% chance of illness.
All other sites have had green readings all summer and have no cautions. Those sites are: Lake Hawea at the Holiday Park, Lake Wanaka township, Lake Hayes at Mill Creek, Lake Wakatipu at Frankton Bay, Hampden Beach at the campground, the Waikouaiti Estuary, Lake Waihola, Kaka Point and the Catlins at Pounawea.
Mr MacLean said the water sampling was generally done weekly, although testing scheduled for December 26 and January 2 was done late because of delays and closures on statutory holidays.
The ORC was satisfied its weekly testing was sufficient, he said.
"Usually sampling occurs on a Monday and the results come into the ORC on the following Thursday, after which they are automatically uploaded to the Lawa site."
• To view water quality readings click here.