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Last month, the council set a goal to make 95% of specified rivers and 100% of specified lakes swimmable by 2030, and 100% of both swimmable by 2040.
Forest & Bird freshwater advocate Annabeth Cohen said if this only included fourth-order rivers and lakes with a perimeter greater than 1.5km, it would exclude many areas where people liked to swim.
Council policy planning and resource management director Tanya Winter said in a statement this week it was the Minister for the Environment who decided which rivers and streams the national policy statement for freshwater management swimming targets applied to.
The council's separate water plan already set limits for E. coli that applied to all waterways in Otago, she said.
"In order to achieve Otago's aspirational swimming targets smaller rivers will also need to be `swimmable' as most flow into the larger water bodies.
"These swimming targets reflect what we have heard from the community over a number of years: keep water quality good where it is good, and improve it where it has become degraded."
The council would consult the community on the targets and the work required to get there, she said.