The court heard that the charges related to two separate incidents. The first in June 2003 involved an overflow from the company's sewage pumping station at Palace Grounds Road in Hamilton after the pumps failed.
The Scottish Environment Protection Agency received public complaints about foul odours from the Cadzow burn. Officers found that the watercourse was scattered with sewage debris.
Scottish Water was fined £1,500 for the discharge. SEPA said that the discharge could have been prevented if the company had had a fully functioning telemetry system to warn of failures.
The second incident affected the Skelly Gill in Larkhall through much of August 2003. Again, residents complained of a strong sewage smell on several occasions.
An investigation by SEPA found that sewage was overflowing into the stream due to a restriction in the foul sewers. When sewage levels rose they overflowed into surface water drains through a connection under a manhole cover. The drains led to the watercourse and caused intermittent pollution.
Environmental health officers issued warnings to avoid the stream which was full of sewage fungus and suffering severe organic pollution.
Scottish Water was fined £3,500. The two offences bring the company's total pollution prosecutions this year to four, with fines of £20,500.