Local government lobbyist usually are regarded by Congress as wanting only one thing in life - all the federal funding they can get.

Yesterday, the National Association of Counties departed from the usual pattern by bluntly tellung Sen. Edmund S. Muskie (D-Maine) that money, even $9 billion of it, isn't everything.

At issue is an amendment tacked on by Muskie to the public works bill that authorizes $9 billion for builsing municipal sewer treatment projects during the next two years under the water pollution construction frant program.

The money is intended to enable all counties and municipalities to bring the water and treated sewage they discharge up to secondary treatment standards by July 1 of this year. This means water from which 85 per cent of the impurities have been removed. It is safe for fish to swim in, although not for human beings to drink.

But more than 50 per cent of the country's local governments will not be able to meet the July 1 deadline. County supervisors cited a variety of reasons, ranging from the impoundment of funds by then-President Nixon in the early 1970s to continuing dureaucratic red tape and delays in dispersal of the funds.

The association of counties, meeting here in convention, said that local government face a series of lawsuits from environmental groups unless Congress extends the July deadline for meeting secondary treatment standards by at least one year. The group also asked relief from a provision of the Clean Water Act, authored by Muskie in 1972, which requires that water charges be basedd on user fees rather than property taxes.

This is politically impossible in a number of areas and unnecsessarily costly in others the association contended.

Muskie said Saturday in a tartly worded telegram that the countries had to choose between immediate funding and consideration of the desired amendments at a later date or no funding at all.A letter signed by the association's entire board of directors said this was no choice and asked for both the money and the amendments.

As a result, the meeting of the association yesterday became a dress user fees out of concern that big users, such as industries, won't pay their fair share. Apparently, his refusal to extend the deadline is an effort to reserve bargaining power.

But the House, which passed the county-backed amendments last year, is expected to favor them again. Majority Leader Jim Wright (D-Tex.) yesterday urged the supervisors to this end.

"There are 535 people in the U.S. Congress and Sen. Muskie is only one," said Wright to loud applause.

Not content with taking on the author of the Clean Water Act, the association decided also to take on the Carter administration.

The organization's board voted to back Congress in seeking restoration of 19 water projects that President Carter wants deleted from the budget.