Strathclyde Loch in Strathclyde Country Park is to host hundreds of athletes taking part in the triathalon when the Glasgow Games begin in July.
Green algae, which can appear after a prolonged period of hot weather such as seen last summer, had appeared in a confined area of the loch but no traces of the algae or other harmful substances were found in tests conducted earlier this week.
A large barrier was built at the end of last year at a cost of £370,000 to make the water safe, but it has emerged that the structure was overwhelmed by the recent bad weather.
The excess volume of water caused tears to appear in the barrier, which is made up of a pontoon, anchors and a low permeable membrane, and it has been replaced at a cost of around £45,000.
Paul Jukes, North Lanarkshire Council's Executive Director of Regeneration and Environmental Services, said that problems occurred after prolonged rainstorms caused the water level in the loch to rise to its highest level for decades.
He said: "During the storms at the end of last year, the exceptionally high rainfall caused the water level in Strathclyde Loch to rise to its highest level since 1994. As a result, on December 30, the barrier installed in preparation for the Commonwealth Games triathlon event sustained some damage. A replacement barrier has been installed and is complete."
Algae, which can cause skin blisters, vomiting and abdominal pains, caused organisers of the Great Scottish Swim to move the event to Loch Lomond last year, while 57 swimmers fell ill in 2012.
Around £1.2million of funding from the local authority and the Scottish Government has been set aside to tackle the waterborne menace, including the barrier and a further £900,000 to pay for UV treatment.
Tests on the loch carried out this week did not find any traces of the algae or other harmful substances and it meets standards which would allow the competition to go ahead.
Mr Jukes added: "Water tests confirm the water quality meets the International Triathlon Union standards for triathlon events.
"We are continuing to prepare Strathclyde Park to welcome athletes and visitors as a proud host venue for the 2014 Games."
Commonwealth Games officials said they were confident Strathclyde Loch remained a "world-class" venue and that there would be no problems when the triathalon, which features a 1500m (1640yd) swim, 40km (24-mile) bike ride and 10km run, goes ahead.
A Glasgow 2014 spokesman said: "We are aware of recent remedial works at Strathclyde County Park and are continuing to work with our partners including North Lanarkshire Council to ensure the loch continues to be used for sporting and recreational purposes and as the Triathlon venue for the Glasgow 2014 Commonwealth Games.
"Strathclyde Park is Scotland's premier watersports centre and a proven world-class Triathlon venue."