I anchor inside the lagoon all the time, so I disagree with @Jeffthornton's opinion about nobody here having experience.
The lagoon has two sides - the Dutch and French; both have different rules.
You can enter the Dutch side and drop anchor anywhere outside of the marked channels and the marked runway exclusion zone. There is not a huge amount of space available. My boat draws 8.5 feet so my options are very limited, but with a shallower draft you can almost always find a spot, even in high season. You can yellow-flag in and anchor before clearing in. The fees for the bridge and for staying in Simpson Bay are published and depend upon the boat length as well as the duration of stay. All of the mooring balls inside the lagoon are private and may not be used without permission. Some are available for rent. The bottom is muddy and there are shallow areas to avoid (I've help pull many a boat off the one close to the Dutch bridge).
The French side is much larger and there's a lot of room to anchor (although there are also a lot of boats). There is no weekly/monthly charge, so it is more popular with the cruisers and liveaboards than the Dutch side. There are mooring balls, but they are also private and cannot be used without prior permission. You can enter the Dutch side and then transit through the Causeway bridge; or use the French side bridge and channel if your boat draft (and nerves - the channel is narrow, poorly marked and shallow) is up to it.
Everything that Zanshin says is correct. I'll just add a little more info though. The bottom is very soft mud in places and you need to check that your anchor is really well set. Also, have the deck wash ready when hauling up as the mud clings to the chain (and it stinks) so you really want to be ready to give it a good clean as it comes up. A great place to spend time and if you need work done on your boat, there is nowhere better in the Caribbean.
I assume the lengths of stay are the same if I arrived by air? Yes - but lengths of stay for people are quite generous on the Dutch side (and can be extended), and as an EU-Citizen I've not even bothered to check the French side rules
Are there mobile services for pumping tanks? No, there are not. All the liveaboards flush overboard.
What is the water clarity in the lagoon for checking the boat underwater? It depends where you are anchored. The water around the SMYC is quite clear and people swim around in it - but it is right next to the bridge and has good flow. Generally, swimming in the lagoon isn't a good idea.
I saw where a couple had some theft on their boat, would you say this is a frequent/rare thing to worry about? Theft is an issue inside the lagoon. It helps to know your neighbours and yachties are a closed group and keep an eye out. There's the daily morning VHF network to discuss security topics.
Is dinghy theft a big worry? Yes. Lock it or lose it when anchored. I never bother locking it at the SMYC or Soggy Dollar, though. Those places are generally safe.
Is it difficult to get space in a yard to make repairs? Not really.
Is it difficult/expensive to have parts shipped to the island? Any difference shipping to one side or another? Very cheap on the Dutch side. Nobody ships on the French side. Use Tropical Shipping or 4-Star Cargo and you can choose air freight or cargo ship depending upon how quickly you need stuff. It is dirt cheap from Miami - two air freight flights a week and several cargo ships.
Are marina slips impossible to get? Not at all. But they are not necessarily cheap. Monthly rates are a lot cheaper, and one can negotiate. [/quote]
Marina Fort Loius round in Marigot on the French side was really cheap when I was there last May. Almost empty as they still hadn't got power properly restored to all the pontoons after the hurricanes a few years back.. Don't know if that is still empty but it is a great place to stay outside of the lagoon.
Switching to around the island, which beaches and bays are good for day anchoring and overnight anchoring? Which ones are total no-nos from overnight anchoring?
West side is of course more sheltered from wave action. My personal preference is Marigot and Grand Case for good holding and proximity to restaurants/shopping. Anse Marcel is quieter with less ashore but very safe and pleasant. I don't really know the east that well, Zanshin will help with that I'm sure, but the one time I anchored overnight in Orient Bay wasn't a great experience as conditions changed in the middle of the night and became pretty uncomfortable.
My favourite is Grand Case - I've spent months anchored there After that it would be Simpson Bay, then Friar's Bay and Marigot. Anse Marcel can have a swell for monohulls, no issue for cats. I like Tintamarre, but usually only anchor/moor there in settled conditions. I've never tried Orient Bay / Cul de Sac and that about covers the east side anchorages. If there's a north swell coming in then inside the lagoon is the only comfortable anchorage. I keep on wanting to try Philipsburg but haven't done so yet, even though it is just around the corner from Simpson Bay, and it looks like good holding in shallow water. But Grand Case is by far the best anchorage. You can be a kilometre out and have 20 feet of water with good sand, and head in close to shore and the dinghy dock and still have 20 feet of water with good sand. That's hard to beat! The only issue is that sometimes the wind funnels through parallel to the GC airport runway and blow through the anchorage. A couple of years back I woke up after a gusty night to find my dinghy with 20HP outboard had flipped during one of those gusts! And Grand Case has always had the "dinghy dock of death"...
Thanks as well, Zanshin & Jeannius. Learned a lot in short time.
How bout St Barts? Same bag of questions. Is the ride more often rough between the two islands. Our one time by power boat was horrific. Our worst time in any boat on any body of water.
The don't call it the "St. Barfs Express" for nothing. Ile Fourchue is uninhabited and has free well-maintained mooring balls. I stop there every trip as I love that anchorage. Then comes my favourite anchorage in the Caribbean, Anse Colombier. There are mooring ball fields (again, free and well-maintained) and one can anchor there. I avoid the balls on the south side as the wind can swirl around at night and once I had to cut away my mooring line to untangle myself. When the weather is settled it is easy to dinghy all the way into Gustavia (assuming your dinghy planes...). Anchoring outside of Gustavia can be a challenge as it is quite crowded, and all of the mooring balls are private.
The reason it was rough for you was the speed of the ferry. It can get a bit choppy between St. Martin and St. Barths in a sailboat, but nothing particularly bad and it is only 30KM from Simpson Bay to Gustavia.
Back in the day, before the power ferries, the catamarans who used to perform the ferry service to St Barth could have their days too. More so for those who were on their 3rd Heineken or Rum Punch before the cat left P’burg harbor.