The Clare river is now being investigated by Galway County Council as one of the possible main sources of the cryptosporidium bug in the drinking water supply in Galway city and the surrounding area.
It is believed that flooding of the river late last year and earlier this year led to large amounts of animal and human waste being discharged into the river, which flows into Lough Corrib at a point less than 10 miles north of Galway city.
Galway County Council director of services Jim Cullen said investigations were now focusing on the river, and officials were carrying out aerial inspections in an attempt to identify potential pollution sources along the river, which stretches 50 miles north past Tuam and into counties Mayo and Roscommon.
It is believed there are a number of untreated and poorly treated sewage systems which are flowing into the river.
This includes the town of Claregalway, now one of the main commuter towns near Galway city, which has no central sewage treatment facility.
"It's had a definite impact," Mr Cullen said of the Clare river, but he said there is still no evidence pointing to one main source of the bug, which has contaminated the drinking water supply of more than 90,000 people in the city and surrounding area.
Other causes are believed to include two sewage treatment facilities at Oughterard and Headford, where largely untreated human waste is flowing into the lake. Contamination from farming along with waste flows from septic tanks have also been identified as contributing to the problem.
However, yesterday Galway County Council said the primary cause of the contamination is believed to have been record rainfall which increased the amount of waste flowing into the lake in the last six months.
"Normally the Clare river wouldn't be a problem, but it was in significant flood in the early part of this year," Mr Cullen said. "It is inevitable that there would have been a wash or flood of contamination into the lake."
Figures show that average rainfall in the last four months of last year was 50 per cent higher than the average for the previous 40 years.
The council is currently working on increasing the supply of water from a cryptosporidium-free source at Luimnagh north of Galway city, which could be in place by mid June.
It came as Green Party leader Trevor Sargent called for a moratorium on all additional housing development in the areas of the county which are feeding sewage into watercourses, including Oughterard and Claregalway.
Last night at a special meeting of Galway City Council, members were informed of plans to provide cheap bottled water to residents in the city. The council will be paying for a subsidy system where shoppers will be given one bottle of water free for every bottle they buy.
The offer will apply only to Galway Mineral Water and will be available in certain shops, including Tesco, Dunnes Stores, Nestors and Joyces, Galway city manager Joe McGrath said.
The cost of the additional water will be paid for by Galway City Council. The council said it has no plans to introduce a similar subsidy system for the county areas affected by the outbreak.
The council has also asked the Government to introduce a voucher system to provide free bottled water for social welfare recipients.
There is increasing concern in the city about the potential impact of the ongoing water boil notice on tourism, although tourism chiefs have insisted that the water crisis had no discernible impact on visitor figures during the Easter break.