The Herndon and Fairfax City councils have approved a new, $1.6 million, five-year rate agreement that raises water costs to Herndon by about 6 percent a year through 1986.

But Herndon Town Manager Edwin Martin said this week he hopes residential water bills will not have to rise. He said he bases his hopes on the savings the town expects to make by plugging leaks in underground pipes and the fact that one town subdivision, Hunter Woods, soon is expected to get its water from Fairfax County rather than Herndon.

Fairfax City, which pumps its water from Goose Creek in Loudoun County and pipes it through Herndon, signed a 10-year water agreement with the town in 1976 that called for renegotiating the rate in 1981. The negotiations were concluded only recently.

The rate charged to the town is a wholesale rate for up to 50 million gallons a month, with a penalty of $3 per 1,000 gallons for any additional water used. The town, which has been averaging less than 40 million gallons a month, charges residents about 60 percent more than it pays for the water, Martin said. He said that the additional charge covers maintenance and operation costs for the town water system.