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.