Horizons Regional Council hopes to have 70 per cent of large rivers and lakes in the region healthy enough to swim in by 2030 - 10 per cent less than a national target of 80 per cent.
The Horizons target rises to 80 per cent by a decade later, with the national target at 90 per cent.
The National Policy Statement for Freshwater Management directs all regional councils to set targets to improve the quality of fresh water.
Horizons chair Bruce Gordon said Horizons targets would contribute to national targets.
The regional council's new targets, while lower than national targets, are higher than they had been previously, due to a 2017 amendment to the National Policy Statement.
Gordon said modelling for the Ministry for the Environment estimates work already planned will see the length of rivers in the region suitable for swimming increase from just 43 per cent to 60 per cent over the 12 years to 2030.
"While this modelling does not take into account factors such as climate change, economic or social drivers, or future changes to policy, Council has agreed to aspire to higher targets of 70 per cent by 2030 and 80 per cent by 2040," he said.
He said the council was aware significant investment would be needed to meet targets higher than the current modelling predictions, but recognised its communities want better water quality, which is why it has set ambitious targets.
"While our region is currently below the national average for swimmability, we are seeing a faster than average improvement," Gordon said.
Horizons natural resources and partnership group manager Dr Jon Roygard said in 2016, the council had upgraded their swim spot monitoring programme from 17 to 83 throughout the region.
"The bacteria and cyanobacteria results are made available to the public on Horizons and Land Air Water Aotearoa (LAWA) websites, so that they can make an informed choice and about when and where to swim in our region," he said.
"An independent report conducted by LWP Ltd earlier this year showed strong evidence for regional improvement in sediment and E. coli measures."