Swimming in an area of St Paul's Bay 'is not recommended' because of possible contamination, the Environmental Health Directorate said on Saturday.
It warned that if contaminated, the water could present a risk to bathers' health.
The directorate said that signs had been affixed close by indicating the affected area and would be removed once the quality of the water had been assured.
The affected area appears to lie between the Buġibba Battery and Buġibba Water Park, close to the Bay Square Cafe, according to an image provided by the directorate.
Saturday's warning comes amid a summer of beach closures due to contaminated water - some lasting longer than others.
In May, popular tourist spot Balluta Bay was closed after becoming contaminated with Escherichia coli, or E. coli, and Enterococci, leaving visitors disappointed and businesses impacted.
Last week, Times of Malta reported that despite the risks to human health posed by the contaminants, which are associated with sewage leaks and feces, no fines have been handed out by health authorities.
The health ministry has attributed the Balluta contamination to a stormwater tunnel exiting into the sea in the area.
May also saw a section of St Paul's Bay near the government school closed because of a sewage overflow.
Meanwhile, St George’s Bay in Birżebbuġa was closed for a second time last month after the water became contaminated with sewage following a blockage in a nearby public toilet.