Balluta Bay has been declared unsafe for swimming after water testers detected the presence of E.Coli and I. Enterococci bacteria.
Both types of bacteria are generally considered to be indicators of sewage or animal waste contamination.
The Environmental Health Directorate issued the bathing warning on Saturday morning, saying bathing was not recommended in the area until further notice. It said it could not predict how long it would be until the warning was lifted.
The directorate said that it was investigating to determine the source of the contamination.
Balluta Bay suffered a similar microbiological contamination issue almost exactly a year ago. On that occasion, it took roughly one week for authorities to declare the bay safe for swimming.