Currently, overall swimmability in Hawke's Bay is 65 per cent of rivers and 68 per cent of lakes, but meeting the draft targets was "realistic and achievable", a paper before council noted.
Doing so won't be cheap; the report estimated the annual cost of the work at $10.16 million, plus another $4.52m expected for extra work.
Some work is already underway, while other work will come under parts of the council's Long Term Plan 2018-2028.
In Hawke's Bay the main source of e.coli - which is used to measure "swimmability" - is ruminant. The main point-source of discharges are sewage.
Existing problems are expected to be addressed through ongoing upgrades and actions at the Waipukurau and Waipawa treatment plants, Takapau Waste water treatment plant and Wairoa Affco meat works discharge.
Stormwater treatment wetlands in the Napier area, including the Ahuriri Estuary and Purimu stream, could reduce the e.coli load by 80 per cent.
In rural areas, attention would be paid to dairy effluent management through measures already in place to ensure effective storage, and deferred irrigation.
The Tukituki plan was also being implemented, and 240 of the required 1100 farm management plans were completed.
Applauding the "ambitious" target, Forest and Bird Freshwater Conservation Advocate Annabeth Cohen urged the regional council to go further.
She said the target might not include all waterways, and places people swam, and the targets "mean nothing" for fish, insects, or plants - as swimmability generally referred to E. coli and applied to human health.
"Currently, 74 per cent of New Zealand's freshwater fish are at risk or threatened with extinction.
"Point source pollution means nitrate levels are likely to be high and oxygen levels will be low. Fish don't have the choice to find another swimming hole."
While the council was moving to address point source discharge pollution, she said they were disappointed there was little mention of agricultural runoff.
"This is a real problem in stream health in New Zealand, especially the Hawke's Bay region where irrigation exacerbates the problem of pollution running off land into water."
The draft regional targets need to be made publicly available by March 31, and final targets available by December 31.