The city is pumping $35 million worth of improvements into Jack's Pond in Great Kills.
The plans call for 90 new catch basins, more than a mile of new storm sewers, and more than two miles of sanitary sewers.
Officials said the improvements will reduce street flooding and enhance Jack's Pond to better filter itself.
The sanitary sewers also mean 51 nearby homes can stop using septic tanks and connect to the city sewage system.
Work is now underway by the City Departments of Environmental Protection and Design and Construction.
It's expected to be complete in 2020.