In the last 10 years more than $250 million has been spent to improve the health of the region's freshwater.
Across 36 sites where freshwater is tested, the level of faecal coliform bacteria has reduced at 22 per cent of sites.
The amount of nitrogen in water has reduced at 58 per cent of sites, the amount of phosphorous has reduced at 28 per cent of sites and the amount of sediment in water has reduced at 19 per cent of sites but increased at eight per cent of sites.
The improvements are more marked in the Manawatu catchment, which has been the focus of the Manawatu Leaders' Accord.
The council tests water at 85 swim spots weekly during the swimming season, and 80 per cent are swimmable in summer.
District and city councils across the region have spent $216.7 million improving their wastewater discharges. There's more to come, with 27 wastewater treatment plants up for renewal and improvement.
Whanganui is to spend $41 million on a new wastewater system. The Rangitikei and Ruapehu councils have a small rating base and particular challenges paying for theirs.
The Whanganui River's greatest challenge is turbidity - the amount of eroded sediment in the water. The Whanganui Catchment Strategy aims to change that, and Dr Roygard is keen to hear from farmers who want grants or help to control erosion.
Horizons also has a bid in to Government, for work in the Whangaehu River catchment. And Mowhanau Stream has been a focus for a while.
The situation with coastal lakes is more complex, Dr Roygard said, because they keep and cycle nutrients and are subject to algal blooms. The council tests four of them weekly in summer, and is undertaking research.
Māori people are also active in protecting water. Iwi groups are spending $3.1 million across the region on improvements.
Improvement is certainly needed. Just like the rest of New Zealand, the only waterways rated excellent in the Horizons Region are headwaters coming out of national parks. They are the upper Rangitikei and Manganui o te Ao rivers.
The changes to national freshwater policy will be woven into the council's existing programme, Dr Roygard said. One of them will require smaller waterways to be fenced, to keep stock out.
Dr Smith said Government aims to have 90 per cent of New Zealand waterways swimmable by 2040. But he changed the definition of swimmable to include more faecal coliform bacteria than the national standard Horizons had been using.
The council doesn't intend to change the way it rates swimmability.
It will keep its "traffic light" system, with a green light for GO when there are less than 260 bacteria per 100ml of water, an orange light for caution when there are 260-540 bacteria and a red light for STOP when there are more than 540.