The First Minister said it was "critical" that the loch earmarked for the open-water swim in the endurance trial at the Glasgow games is cleaned up to stop a repeat of recent problems.
Salmond made the comment four days after 57 out of 70 swimmers fell seriously ill after an event at Strathclyde Loch in North Lanarkshire.
No-one was hospitalised but they suffered vomiting and diarrhoea. Some tested positive for the norovirus winter vomiting bug. The loch was deemed "well within acceptable open-water swimming guidelines" two days earlier, but heavy rain led to contamination.
The water was closed for "immersion sports" for six weeks as a result of the incident.
Despite a history of pollution, the loch is to host the 1500m swim which starts the triathlon in July 2014. Minutes from the Scottish Government's Glasgow 2014 Strategic Group, which the First Minister chairs, show the pollution threat in the loch is now "one of the principal risks affecting Games delivery".
The minutes show Salmond personally "highlighted the resolution of this issue as critical". Two alternative locations had been identified, but Strathclyde is still the preferred option.
The strategic group is now to receive regular updates on the problem.
Scottish Water and the Scottish Environment Protection Agency are working on a £150,000 plan to improve the loch water before 2014.
A Glasgow 2014 spokesman said: "It is a matter of good Games planning to have contingency plans across the theatre of operations."