The seawater at Balluta Bay is safe again, the Environmental Health Directorate said on Monday.
It said it was lifting health warnings after repeated tests of seawater samples.
The bay had been off limits for swimming for most of the summer, with warnings having been issued in May and June because of sewage seepage and the presence of after E coli.
Late last month the health ministry said the contaminated water came from a stormwater tunnel that flowed into the sea.
“The required works were extensive as this tunnel had to be cleared of a lot of debris to determine the source of pollution. This flow of contaminated water has now been controlled,” a ministry spokesperson had said.