An unknown "soapy substance" combined with warm weather and low water levels is believed to be behind the death of scores of fish in a creek in Melbourne's south-east.

Melbourne Water said it has removed about 40 dead carp from the duck pond in Gardiners Creek in Ashburton after community members alerted the Environment Protection Authority to the deaths.

One witness, Jennie Schopfer, said: “It looks terrible. Ducks and herons amongst the stinking dead fish corpses.

"Did someone dump chemicals in the waterway while they think everyone is in lockdown?"