The green colour in Balluta Bay is not the result of contamination from the sewerage network, the Water Services Corporation said, without offering an explanation of what had actually caused it.
The bay turned green over the weekend, raising a wave of complaints from neighbouring residents and visitors.
Bathing in the bay has been prohibited for practically two months, with the Environment Health authorities having first issued a warning on May 24 after finding microbiological contamination of E.coli and I.enterococci.
The WSC said that when it received the initial reports of contamination it launched an investigation which confirmed that the contamination was unrelated to its network.
It transpired that a stormwater tunnel in the area was in severe disrepair, resulting in contaminants flowing directly into the bay.
It said that although the maintenance of stormwater tunnels does not fall within its remit, it proceeded with the required interventions to mitigate the issue. The tunnel was cleaned and parts were rebuilt.
A large amount of debris was removed, ranging from stone boulders to wooden planks, nets and miscellaneous discarded items.
The green colouration occurred days after the cleanup.
The WSC said it again analysed the situation and once again confirmed it was unrelated to its network.
It did not say who is responsible for the maintenance of stormwater tunnels but regretted what it said was unfounded claims on social media that the seawater discolouration was the result of raw sewage coming from its network.
The relevant authorities will determine the reopening of the bay once the necessary testing is completed, it said.
The Environment and Resources Authority said on Sunday that it was investigating the situation in Balluta to determine the cause of the green seawater.
It pointed out that algal blooms may occur due to high temperatures and reduced water circulation, conditions typical of heatwaves such as the one Malta is currently experiencing.