The incident at the firms' Bulmer’s cider plant in Hereford during August 2014 happened after a container of ammonia-contaminated water was emptied to a surface water drain which connected to the Widemarsh Brook.
At the time it was estimated that between 2,000 and 3,000 fish were killed including minnows, juvenile chub & dace.
As a result of an enforcement undertaking, Heineken has agreed to give a total of £150,000 to the Wye & Usk foundation and £10,000 to Yazor Widemarsh & Eign Brook restoration project.
Dave Throup, Environment Agency spokesperson, said: "It’s very unfortunate that a significant pollution of one of Hereford’s main watercourses happened as a result of Heineken’s actions.
"However, we are pleased that the company is planning to make a positive contribution to the county’s environment by offering this enforcement undertaking."
The firm has also paid more than £12,000 to cover the Environment Agency’s legal costs.
