I've lived aboard quite a bit during my adult life, and until a few years ago, I always had canine companions.
The first time was aboard a 29 foot sloop back in the early 1980's when a very ugly divorce left me no choice but to live aboard or give up the boat. Anyway, I had my two Shetland Sheepdogs and we did fine. Kelpie, the male, was about 25 pounds and Shannon, The Queen of all she purveyed, was about 18 or 19 pounds.
Kelpie had gone on his first sailing trip aboard my O'Day Day Sailor, a trip from Long Beach to Catalina when he was 10 weeks old, and it was obvious that I'd chosen an appropriate name. Kelpie was a sea dog to the bone. He loved it, and never in his life got seasick, no matter how rough it got. Shannon did okay most of the time, but suffered occasional mal de mer in rough weather. She 'joined the crew' after the O'Day, and learned sailing on a 29 footer.
Both dogs used the forward deck when we were anchored or it was really smooth. I put down an exceptionally aggressive non-skid on the deck, because I hated slipping and it gave the dogs good traction, too. I did, after Kelpie followed me in swimming, put on life nets from the bow rail to the stern rail.
I took that little 29 footer and did a single-handed crossing from Long Beach to Honolulu, and Kelpie ended up being the best crew I have ever sailed with. I'd do my sleeping during the day, waking up for a noon sextant shot, then napping again until just before dusk. While I was sleeping, my little canine crewman stayed on deck, lazing in the shade of the sails and watching the horizon. When a ship came into sight, he'd start barking, and get me up. On a couple of occasions, after a rough night with squalls, I was sleeping harder than normal, and if I didn't come on deck quick enough, he'd jump down and use his long nose to poke me until I was awake. On another occasion, a line on the self steering frayed through and broke. The little dog must have understood it meant trouble, because he absolutely started raising Caine until I came up on deck just in time to prevent an uncontrolled gybe.
Shannon kept me company at night. When the wind was right, she'd start fussing when she smelled the exhaust from a ship that was still over the horizon. Otherwise, she almost always spotted running lights before I could, and would start barking and wagging her tail.
Cleaning up after them was never a problem. A bucket of salt water took care of most problems. When it was rough and they couldn't go topside, they went in the fiberglass head. A little cleanup was all it took.
Many years later, I lived aboard my old Morgan 36T racer with another Sheltie, Skipper.
Like Shannon and Kelpie, he'd been raised sailing, so living aboard was fine with him. I'll say this now about Shelties: the are happy living just about anywhere. If they have acres to prowl, like Skipper did at a friend's place, he was okay with it. When we were waiting for the house to be built, we lived in a tiny efficiency apartment and he was okay with that, too. Living aboard was no big deal for him.
Skipper would 'say hello' to our liveaboard neighbors with a friendly bark and wag of the tail. He would also let strangers know they weren't welcome, and the barks were very distinctively different. The neighbors spoiled him rotten. When I was at work, he came and went below as he wanted to: I left the bottom drop boards out. He climbed the companionway ladder with no problem, and would jump onto the quarterberth to get down. The Marina rules said that all dogs had to be on a leash at all times. That wasn't a problem, either. He just carried his own leash was all. I rubber banded a 6' nylon 'show lead' into a bundle, and he carried it in his jaws. Knowing that the little guy was, if anything, too friendly, the Marina manager let us get away with it. The rule said he had to be on a leash. It didn't say who had to hold the leash, right?
Anyway, Skipper and I lived aboard for nearly five years, and even went cruising in the Bahamas. Like with Shannon and Kelpie before him, he shed heavily twice a year, so he got extra brushings and the vacuum got a workout.
Was it worth it? You bet. Would I do it again? Yes. Any suggestions? Sure. Here they are: Buy your little friend the best life jacket that you can buy, and make them wear it when the boat is underway. Dogs are good swimmers, but they are not strong swimmers. They get tired quickly, because they are basically running the water. Buy some of that incredibly expensive SOLAS reflective tape and sew it onto their life jackets, and buy a strobe light that is salt-water activated and attach it to their life jackets.
Keep their toenails trimmed close, because walking on a fiberglass deck is horribly hard on their feet. (That's from a DVM who was a liveaboard friend!)
Keep them brushed and clean. They're going to get wet, and we all know what wet, dirty dogs smell like.
Keep them on a steady diet of good food. It will keep their stools solid and easy to clean up. Skipper was being spoiled rotten by our neighbors and part of that was he was getting 'nibbles' from everyone. One guy, who said he'd never liked dogs before, even bought Skipper a box of doggy treats and would feed him one every day. It was cute, and fun, but Skipper's tummy didn't necessarily like it much. Loose or runny stools on a rainy day with everyone trapped below is not pleasant. I finally made a sign that said, "Please don't feed me any treats. The Captain says I'm getting fat!"
Skipper 'signed' it with a little paw print and I hung it on the bow rail. Most people laughed and cooperated, but I think that the 'dog hater' cheated occasionally.
Take them for walks every day and let them burn off their excess energy. Play ball with them, take them swimming, whatever, but keep them active. They'll be happier and live longer.
Keeping an eye on the boat for you is fine. That's what a watch dog is for, but it has to be reasonable. Having a dog barking and raising H*** for ten minutes just because someone walked past is unacceptable, and that's living aboard or living ashore. Prolonged barking should be a 'shout for help' when there is a real problem, like some teenaged jerks untying your docklines, such as happened to me down in Fort Lauderdale's city marina on the New River. I was lucky. Skipper raised so much of a racket he chased them off even before I could get on deck, .45 in hand. A big 'booze cruise', three deck boat a hundred feet from me hadn't been so lucky, and ricocheted down stream for a mile before the Lauderdale Marine Patrol, Sea Tow and TowBoat US could get her under control. I heard at Lauderdale Marine Center that the big boat had caused about 3 million in damages, and drove the owners broke because their insurance didn't want to pay off. They never caught the kids, naturally. (There's another lesson in this. When I'm in the city marina now, I put a 'waist' chain with locks at both ends.)
Remember that dogs are hard-wired to please you. Remember that you have to be their 'Alpha' to make them behave. I know it sounds silly, but if you're going to be living aboard, watch 'the Dog Whisperer' on Nat-Geo. That guy is an absolute wizard at teaching you how to be the Big Dog.
Some people have recommended big dogs. I absolutely disagree with that. Your canine buddy will, sooner or later, go overboard. Maybe, like Kelpie, he just wanted to follow me in for a swim, or because he thought I was in trouble. A good dog will always do what he thinks he has to to help his Big Dog. Kelpie probably thought I'd fallen overboard and followed me in to 'save' me. What actually happened was I had forty pounds of soggy fur and dog that I had to get aboard without any help on deck. That was tough for me, and tougher for him because I ended up picking him up by the scruff and basically throwing him aboard. Now imagine if that had been a big Golden or some other 70 pound dog. Even worse, imagine a 110 pound Rottie! How would you get them aboard? That's like picking up a small human, and a dog will start panicking before very long when he realizes he can't get out of the water, which makes it worse. You can handle a panicked human. I defy you to try and hang on to 100 pounds of frightened dog.
So pass on the big dog breeds. Goldens are great, but they just don't belong on a boat, IMHO.
Good luck, and enjoy living aboard. And don't forget to take your canine buddy with you.
S/V Island Breeze