The City of Beacon had two manholes on an aging sewer line replaced Tuesday, the first step toward fixing raw sewage leaks into the Fishkill Creek, City Administrator Joseph Braun said.

Like many sewage systems in old settlements, Beacon's system often overflows during heavy rain storms. Old and cracked pipes, connections to storm sewers and illegal sump pump hookups allow rain water that isn't meant to flow through the sewage pipes to overwhelm the system.

The city also will pay to have a sewer line along the creek replaced. That will be completed by a Department of Transportation contractor during the repaving of Route 9D.

In addition, Beacon is working to engineer a solution to a third overflowing manhole. It has set up eight flow meters throughout the system in an attempt to pinpoint sections of pipe that take on storm water.

"We're praying for rain right now," Braun said. "That will help us really understand what is happening."

The cost of the fixes was not available Tuesday.

The Garrison-based environmental group Riverkeeper threatened to sue the city for violations of the Clean Water Act when it learned of the leaks into Fishkill Creek, which empties into the Hudson River. It filed a notice of intent to sue Sept. 1, but has not sued yet.

"The goal is always to fix the problem," said Sara Froikin, a Riverkeeper program associate. "The goal is never to just bring a lawsuit."