New Yorkers could be drowning in a 50 percent water-rate hike if the city is forced to build a massive $6 billion filtration system in two years, Comptroller Alan Hevesi said yesterday.

"It's a huge expenditure," Hevesi said. "It would be a blow to low-income homeowners. It would be a blow to small landlords ... It would be a blow to the continuing success of the city."

Under an agreement with federal authorities, the city would be required to build the system if it can't fix pollution problems around its 19 upstate reservoirs by 2002. Water and sewer customers would face a 22 percent increase during just the first four years after the city starts paying off the debt - a jump from $450 to $549 a year for the average residential user, and from $4,501 to $5,491 a year for the average commercial user.

Rates could go up a total of 50 percent over the three decades it would take to pay for the filtration system, Hevesi said.

Mayor Giuliani dismissed concern that the city might not meet its deadline, saying the city is well on its way toward fulfilling its 1997 pledge to clean up the reservoirs.

"The reality is that the city is ahead of schedule and should be able to meet the [May 2002] target date," Giuliani said.

The comptroller's warning came a day after the federal Environmental Protection Agency said the city must step up crucial efforts to protect its drinking-water supply before the deadline.

Both the EPA and Hevesi said the city has to work harder to buffer Westchester's Kensico Reservoir agains