A shampoo spill left a Melbourne waterway covered with foam and the environmental watchdog has fined the company responsible thousands of dollars.

The foam spread across part of Blackburn Lake in January after a 100-litre drum of shampoo spilled into a drain from the Nunawading factory of STN International Pty Ltd.

"The foam pile at Blackburn Lake troubled community members and had the potential to harm aquatic life in the lake," Environmental Protection Authority metro regional manager Dan Hunt said in a statement issued on Thursday.

Shampoo and soap can deprive fish and other aquatic life of oxygen in the water and interfere with their metabolic processes, he added.

The company was fined $8,060.

A waste contractor removed the shampoo from the drain and Blackburn Lake and the company has put in controls to prevent any additional spills.