County Public Health Officer Melitus Kabari said laboratory analysis shows that all springs in the town have particles from toilets.
GWASCO has been trying to clean up River Nyakomisaro, which runs across Kisii town.
Mr Kabari said his department had identified six private developers who have been discharging raw sewage into the river and would take action on them.
GWASCO has only one exhauster that serves both Kisii and Nyamira counties.
The agency said the main water pump located at Kegati, put up in 1977 to serve half-a-million people, can no longer effectively serve the more two million residents of Kisii.
“We have an alternative from Nyakomisaro water supply, which produces 6,000 litres a day,” GWASCO board chairman Benjamin Onkoba said, adding that the water rationing programme would be revised.
ALSO READ: Coffee factories face closure over environmental pollution Mr Onkoba said a Sh2.6 billion loan had been acquired to expand the main Kegati water treatment plant.
“The works begun last year and will be complete in March 2019.
The project will lead to the production of 27 million litres of water every day and will serve residents for 25 years,” said Onkoba.
With the support of the German bank KFW, GWASCO will next month get a water bowser with a capacity of 10,000 litres, which will be available to deliver water at a fee of Sh1, 500, particularly to government institutions.