Great bay can "blow-up" in a matter of minutes, in a way every bit as treacherous as the open ocean. PFd's should be worn at all times in a canoe or kayak or jon-boat. Help from a larger boat can be some distance away , even in little bay. I have canoed, sailed and motorboated Great Bay for 25 years. I always followed the practice of never entering the open ocean without a marine radio. I'm happy to say, I have never needed it for a distress call, but would still not allow myself to be caught without one.I would suggest that for both bays as well. Please note that a radio without a chart of the bay to report your position is nearly worthless.
State Marine safety patrols are so sparse that far inland as to be non-existant.In short, if you get into trouble you're on your own.I've towed numerous powerboats to safety with engine problems, out of gas etc., but all of those people were extremely lucky I happened by and actually noticed them as being in distress. It is not uncommon to spend the entire day on the bay and never be within shouting distance of another boat. A radio + flares should be considered mandatory safety equipmeny out there. The water is Much-Much colder than any you'ved experienced in the Bahamas. The coast guard uses the guideline of 50 degree water 50 minutes in it, 50/50chance of survival. The bay is seldom as warm as 50 degrees.

Almost anywhere on either of the the bays is a 50 minute swim to safety, considering reduced muscle function in cold water.
Also the Route 4 bridge by Great Bay marina has a terrific rip during a tide-turn. I would not attempt that in any of the aforementioned hand-powered vessels.
A number of Years ago a UNH student drowned out there.