Some 18,000 tons of waste and silt have been collected during dredging and a clean-up along the valley floor of Wied ta' Zejta, near Victoria, the Gozo Ministry said.
The works started a few months ago.
Gozo Minister Giovanna Debono, who toured the site this morning, said that a similar clean-up of the valley between Marsalforn and Victoria would be taken in hand this week.
Both valleys include dams for rainwater storage.
The purpose of the clean-up, the minister said, was to enable Gozo to retain more rainwater rather than having it flow into the sea This would benefit farmers and make them less reliant on ground water extraction, which depletes the water table.
She said that rubble walls along the valleys are also being repaired