Once established, the giant water flea is difficult to eradicate or control. 

The best approach to control is to slow the spread and reduce the role of humans in introductions.  Two effective methods are preventing the introduction of exotic aquarium fishes and their water to native habitats and not transporting water in recreational boats.

In some cases, such as in small fishless lakes, the giant water flea can be controlled through chemical means, although resting eggs are resistant.

Stocking larger young-of-the-year fish may also result in biological control of this species.