THERE WERE a few obstacles - some imagined, some real - to be overcome before Cheryl Phipps took command of Harbor Queen, a 1,340-h.p., 83-ton, double-decked sightseeing vessel that takes upwards of 100 passengers on 40-minute rides around Annapolis Harbor.

"When I went to the Coast Guard in May to get my Master's License I thought they might, you know, give a hard time because I'm a woman," said Phipps last week to some people who had come to see her work.

"I was pretty uptight about the written exam. It's in eight sections and if you don't pass one section they won't let you take the next. It turned out OK. The Coast Guard was cool."

Phipps is cool herself. She has big blue eyes and a confident air nicely enhanced by a jaunty cigarette holder and a king-size cigarette. She does not wear a uniform, nobody calls her ma'am and she couldn't be more modest about it at all

As she checked out her boat for the first run of the day, Phipps said her career had its beginning in 1970 when her father gave her a 17-foot runabout. She didn't think then of the water as a profession, but after two unsatisfying years at a community college she turned to it. In April, 1976, she went to Harbor Queen's manager and talked him into taking her on as crew.

Her job was keep the boat clean and to handle the dock lines, and in due course she learned how to operate it.After a year she decided to apply to the Coast Guard for the 100-ton license that would permit her to become its master.

There were three main requirements: she had to be 18, pass a written examination and prove a year's experience in operating the boat.

"The year of experience is the hardest part," Phipps said. "The Coast Guard wants 365 days at eight hours per day. Fortunately, I had logged all my work the previous year and my boss certified it."

Getting her license didn't automatically get her assigned as Harbor Queen's skipper. Here she faced real prejudice.

"One of the owners wasn't all that excited about a woman driving his boat," she recalled. "He didn't think I could handle it. But the manager said 'Hey, watch this guy, give her a chance . . .' and he did and there hasn't been any trouble from the owner since.I became master in June."

Now, on a pretty day in July it's time to shove off and Phipps takes her guests up to the pilot house. Precisely at noon - right on schedule - she tells her deck hands to cast off the lines, blows the whistle and backs Harbor Queen smoothly away from Annapolis City Dock.

Is that the trickiest part, taking it out?

"Landing is. We bring a sister ship in backwards and the first time I tried it I bounced it against the dock. Somebody was telling me exactly what to do, only I got nervous and began using the throttles backwards - reversing the engine I wanted to advance and advancing the engine I should have reversed. I knew I was doing it wrong but somehow I couldn't help myself. I almost cried. I wanted to quit right then. I said 'Forget it . . .' My boss let me alone, though, and I finally calmed down."

Today she couldn't be calmer. The boat moseys around Annapolis Harbor, leaves the Naval Academy to port and heads east toward Chesapeake Bay. There is little traffic and Phipps says that's a problem only on weekends.

"At first I was scared to come to work. I would be shaking all over driving the car in. Now that I'm getting used to it, maneuvering when it's crowded is fun. I back down a lot and don't insist on my rights. So far I haven't had an accident."

After 20 minutes she heads back to the dock. The vessel seems to be moving too fast as it approaches, but at the critical moment Phipps gives her engines a burst of reverse and Harbor Queen snuggles up against her pilings. The lines are tied, the engines are killed, another routine run is finished.The master lights one of her long cigarette.

"It was nice having you on board. Come back when I get a bigger license."

Those inspired by Phipps should know that a Coast Guard license is required by any boater who uses a mechanically powered boat to carry passengers for money. Applicable publications and license applications may be obtained without charge from the Coast Guard's Marine Safety Office, U.S. Custom House, Baltimore, Md. 21202.

The least sophisticated license is the Motorboat Operator, which applies to vessels not more than 15 tons carrying not more than six passengers. Applicants must be 18, pass a test and prove 365 days of operational experience. The application form is CG-866.

The next higher license covers operators of vessels under 100 gross tons. The requirements are spelled out in "Rules and Regulations for Small Passenger Vessels, Subchapter T, CG-323," dated Sept. 1, 1973.

Those who aspire even higher will want to read "Rules and Regulations for Licensing and Certifying of Merchant Marine Personnel, CG-191." dated Nov. 1, 1976.