I can't advise medically but there are a few things I feel competent on.
I'd imagine that you are concerned mainly with two things, enteric tropical disease like typhoid and cholera and mosquito borne diseases.
Lets start with the water
HYGIENE is the way for you all to stay healthy. - Your daughters health
depends on you both staying healthy. That means you should be very careful about what YOU eat both on the boat and ashore. Don't eat left overs unless you are very sure they have been kept sufficiently cool. Don't eat anything ashore that isn't REALLY hot, preferably cooked in front of you. Sterilize fruit in a solution of bleach, 1 tablespoon in a pint of water, wash off with boiled water. Don't eat fruit from shore side vendor until you can wash it. The same of course goes for salad vegetables.
Make sure your water supply is safe and if you are unsure, only drink what you have boiled and allowed to cool. Never have ice in drinks away from the boat. Without a child to worry about, I'd perhaps take a chance in a posh bar but....
For your daughter, breast is still best but otherwise, ensure that you make up a bottle for each feed when you need it, unless you have refrigeration
what can maintain a temperature under 5 degrees Centigrade, (check this before you leave). With solids, cooked food, prepared not more than an hour before, again, unless you have very reliable refrigeration
. OR, like most parents, lay in a supply of baby food in jars. Don't keep any left overs, these are particularly likely to be contaminated with staph and strep type bacteria from the spoon (contaminated in the mouth), these bugs can grow at an alarming rate in tropical conditions.
No swimming in rivers or lakes - the likelihood of faecal contamination is high and there is a possibility of nematode infestation.
Only eat shellfish that you have cooked yourself, avoid fresh water fish
which may have liver fluke metacercarial cysts.
Of course, all food should be kept covered and away from flies.
Moving on mosquito problems - I'm sure that I don't have to remind you about the importance of a mosquito net. I think that on balance an impregnated net is best but you may want to talk to another tropical disease specialist about this. Most mosquitoes tend not to fly out any great distance from the shore so you may want to consider anchoring
out most of the time, a minimum of 300 metres avoids most mosquitoes. In a marina, avoid dusk and dawn exposure as much as possible and perhaps consider always having the baby in a crib covered with a net at those times. I personally would use a pyrethroid insectacide spray below decks in the early evening and then keep all ports
and access ways covered with insect screens.
Talk to your travel advice nurse or physician about vaccinations and anti-malarial prophylaxis.
Hope this is of some help