The general manager of the Washington Suburban Sanitary Commission yesterday recommended a 28 percent increase in water rates that would raise the average homeowner's bill by $49 a year starting April 1.

The six commissioners, who last week failed to approve a 13 percent rate rise when they deadlocked in a 3-to-3 vote, did the same yesterday. The three Montgomery County commissioners favored the increase in their preliminary vote, while their counterparts from Prince George's opposed it.

The new rate increase was included in general manager Robert McGarry's proposed $149 million operating budget for 1981. The proposed budget, if approved by both county governments, would mean a 15 percent increase over this year's $131 million spending level.

Last week, McGarry warned that without a rate increase, the agency would run a deficit of more than $2.3 million by next June and would jeopardize its bond rating.

For several months, McGarry had tried to win approval of an immediate 13 percent rate increase, proposing the measure as an amendment to the 1980 budget. Now, according to WSSC public information officer Arthur Brigham, that effort has been abandoned.

However, the commission's failure to approve a rate rise this year has forced the staff to ask for a far larger increase next year, he said.

An even higher increase -- 33 percent to 36 percent -- would be necessary to generate the operating money if no action were taken this fiscal year, Brigham said.