Earlier this year the Government announced national standards for freshwater, requiring a minimum standard to make rivers safe for wading and boating, and allowing local authorities to set higher standards if they wanted.
The Labour and Green parties want stronger measures to make all lakes and rivers swimmable, and say National's economic blueprint would increase dairying and hurt the environment, which would adversely affect the tourism industry.
National has criticised the Opposition proposals as potentially costing billions.
Ms Adams said the $100 million fund would give councils another option to manage freshwater.
As well as excluding dairy cattle from waterways, National would also work with farmers towards excluding other cattle from waterways over time on intensively-farmed lowland properties.
National has already flagged a $400 million fund for new irrigation projects.
Ms Adams said National could build the economy and protect water quality at the same time.