One Ruamahanga River swimming spot has been marked as unsafe and another carries a caution warning in a list of sites now being monitored for water quality.
The water at the river swimming spot near Kokotau Road, east of Greytown, carries an "unacceptable health risk".
The health risk is determined from the number of bacteria found in water samples.
The level of E-Coli colony-forming units (cfu) per 100ml of water at the spot was on Monday recorded at 580, well above the level required to cause alert, and well up on the previous reading of 46 cfu/100ml recorded on December 7.
The other site - the Ruamahanga River at Morison's Bush near Greytown - carried an "increased health risk" warning but with a recording of 276 cfu/100ml of water, the quality was ruled within an acceptable range.
The high levels were the result of freshes caused by last weekend's heavy rainfall.
The two spots are currently the only measured sites across the Greater Wellington region where the water quality breaches the alert level.
During the summer bathing season Greater Wellington Regional Council, local district councils and Regional Public Health work together to monitor the waterways and keep the public informed.
Greater Wellington posts results from monitoring at popular beach and river swimming spots weekly from November to March using a traffic light system.
The region council is also encouraging river users to keep an eye out for toxic blue-green algae, which may be prevalent during low river flows and warm temperatures.
"We've had no reports of extensive algal mats in the region so far this season, but if we get a decent dry stretch, and river flows decrease and temperatures rise, we may see a return of extensive toxic algal growth similar to that seen in some of our rivers last year," Greater Wellington environmental scientist Summer Warr said.
In January, toxic algae in Waipoua River sparked health warnings at several popular Masterton swimming spots.
The algae can be fatal to dogs and livestock if eaten, and can make humans sick.
Blue-green algae is assessed weekly during summer at 21 river spots throughout the region.
Greater Wellington uses a two-tiered warning sign system to advise river users of the risk from toxic algae.
A medium risk sign means users can still swim or walk their dogs but should keep an eye out for algal mats.
A high risk sign means people should avoid contact recreation and dog walking in that part of the river.
*People can monitor both blue-green algae and water quality warnings on Greater Wellington Regional Council's website, www.gw.govt.nz.
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