She said both the Tauherenikau and the Waiohine, because they were shorter and fast running, were always going to be cleaner.
Greater Wellington Regional Council senior environmental scientist Summer Greenfield said the main source of contamination on the Waipoua River was runoff from intensive agricultural land use upstream.
"For the two sites in the Ruamahanga River the main source is discharges of treated sewage from municipal wastewater treatment plants."
GWRC environmental policy manager Jonathan Streat said plenty was being done to try to turn the rivers' health around.
"The days are gone when regional councils can legislate the environment into shape.
"Everyone living in the Wairarapa Valley upstream of these swimming holes can have an effect on them.
"The community as a whole needs to find the solutions for managing land to improve water quality. That's the best way to get a lasting approach and is what we are doing with the review of our regional plans for managing land and water."
The ministry assessed 210 freshwater beaches and 248 coastal beaches used for recreation based on monitoring data acquired over five consecutive summers.
The beaches were graded to describe their likely condition for recreation during summer based on an assessment of potential sources of faecal contamination.
Mr Streat said the council was setting up a zone committee for the Wairarapa Valley that would set environmental targets for water quality - and methods to achieve that.
"This is not a task that can be done in isolation of industry and the community involvement. It also takes time, water quality won't improve overnight."
Mr Streat said a pilot committee in the Mangatarere Catchment west of Carterton comprising farming reps, councillors, iwi and other residents was in place and working on a management plan to improve water quality.
"Another example of what we're doing right now is with farmers on land and environment plans to identify areas where nutrients and effluent can get into waterways and groundwater and how to stop it."
A new member's bill drafted by Green MP Catherine Delahunty aims to tighten controls on sustained pollution of waterways. It would close a Resource Management Act loophole that allows contaminating discharges with toxic effects and discolouration of waters under "exceptional circumstances".
Ms Delahunty said the phrase had no timeframe and her bill would limit its use to five years.
Extra reporting by Tessa Johnstone
The best and the worst:
Very good: Waiohine River at Gauge
Good: Ruamahanga River at Double Bridges, Waingawa River at Kaituna and South Rd, and Waiohine River at State Highway 2
Poor: Ruamahanga River at The Cliffs
Very poor: Ruamahanga River at Kokotau, Morisons Bush, Te Ore Ore and Waihenga, and Waipoua River at Colombo Rd
