Horizons councillors have set the goal of having the region's rivers 90 per cent swimmable in the summer bathing season of 2040.

Leading up to that they want rivers 70 per cent swimmable by 2030, and 80 per cent swimmable by 2040, with the peak of 90 per cent swimmability in summer.

A motion to aspire to 90 per cent across all seasons in 2040 - New Zealand's national target - was narrowly lost at the regional council's strategy and policy committee meeting on November 13, Whanganui councillor Nicola Patrick said.

She voted for it, along with Rachel Keedwell, David Cotton, Jono Naylor and Wiremu Te Awe Awe. Against were John Barrow, Lindsay Burnell, Gordon McKellar, Bruce Rollinson, Paul Rieger and Colleen Sheldon.

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The targets are a response to government's 2017 amendment to the National Policy Statement for Freshwater Management. It directs all regional councils to set targets. The targets are only for larger lakes and rivers.

If Horizons achieves its target the length of region rivers suitable for swimming will increase from 43 per cent to 60 per cent by 2030.

Councillors know significant investment will be needed to meet the targets, chairman Bruce Gordon said.

"While our region is currently below the national average for swimmability, we are seeing a faster than average improvement."

Horizon's Sustainable Land Use Initiative for erosion-prone hill country and its fencing and planting programmes were starting to make a difference, Gordon said.

"Taking a planned, whole of catchment approach and prioritising effort and investment where it would make the most difference works."

The council monitors water quality at 83 region swim spots every summer, natural resources and partnerships manager Dr Jon Roygard said.

"From early November until the end of April samples are taken from these sites on a weekly basis and sent to an independent and accredited laboratory for testing. They are tested for faecal indicator bacteria including E. coli for freshwater and Enterococci for coastal waters. Our scientists also check each site for phormidium, known as potential toxic algae or cyanobacteria."

Results of the testing are available to the public on the Horizons and Land Air Water Aotearoa (LAWA) websites.

The council also monitors water quality from sites across the region every month, and at some places every 15 minutes. The water is tested for levels of nutrient, bacteria, sediment, clarity and physico-chemical stressors such as pH and temperature.

Sediment and E. coli levels are reducing, but E. coli concentrations generally don't meet swim guidelines in the One Plan. And while rivers are improving in the region overall, Roygard said there was decline at some sites.