Water with less than 130 E. coli per 100ml is equates to an extremely low risk of illness.
Horizons' staff will also be looking at cyanobacteria/bluegreen algae densities. High densities can create a black, musty smelling, slimy mat of algae that covers river stones. People and animals should avoid this water.
Results of Horizons' monitoring are also used on the Land, Water, Air Aotearoa (LAWA) website's national swimming guide.
The samples are only taken once a week, and water quality can change quickly. As a general rule, if the water is clear and it hasn't rained for three days swimming should be okay.
Across the last 10 years the region's water quality had improved in some places, Horizons science manager Abby Matthews said.
Levels of E. coli are better in 17 per cent of waterways, including the Manawatu and Whangaehu. Levels of nitrogen are better in 35 per cent of waterways and worse in 2 per cent, and levels of phosphorous are better in 22 per cent and worse in 7 per cent.
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Last summer Horizons asked people to vote for their favourite swim spots, and offered a spruce-up to the one that got the most votes. Whanganui's Mosquito Point won.
Work is underway there now, with new seating and retaining walls in. Fresh BBQ tables and a changing room will be next.
People commenting on this on Horizons' Facebook page said they would like the Mosquito Point swing replaced as well. One person also suggested toilets.
This summer the council is offering a $1500 adventure package to a person who posts a photograph of a region swim spot.
The photos should be posted with the hashtag #swiminourregion and the swim spot's location tagged to Facebook, Twitter and Instagram.
Everyone who enters will be in the draw for the prize.
