Regarding malaria, the US Center for Disease Control has a single recommendation for the countries of Belize, Costa Rica, El Salvador, Guatemala, Honduras, Mexico, Nicaragua, and Panama, despite the fact the danger of contracting malaria varies greatly from country to country and from region to region within the countries. The CDC recommends taking Chloroquin, which, if you choose to use it, you should start taking at least 2 weeks before possible exposure. (To cover their backs the CDC says a month to 6 weeks.)
Our Costa Rican doctor, who has no bureaucratic needs to cover his back and whose judgment in these matters we have come to respect, does not agree with the recommendation, He points out that while there is a slight chance of getting malaria in Costa Rica, there is also a slight chance of side effects from Chloroquin, which is at least as serious as the strains of malaria that have been recorded here. What we who live here do, if anything, is use insect repellant that contains DEET (diethylmethyltoluamide) when there is a likelihood of getting bitten.(Be sure to follow the precautions on the label.)Not only will this minimize the possibility of getting malaria, but also it will help protect you from getting other insect born diseases---not to mention itchy bites.
While we are talking about prevention of disease, make sure your tetanus inoculation is current.
SOME ADDITIONAL INFORMATION ON MALARIA
According to the latest information (from 2012) malaria in Costa Rica has gone down 75% since 2001. In 2010 there were only eight registered cases. The vast majority of cases used to be in the province of Limon but new prevention measures in that province have resulted in there being only a single case in 2011. There have been no cases of malaria in Tortuguero in the last few years.
There have been no deaths in Costa Rica attributed to the strain of malaria that occurs in Costa Rica.
The last death in Costa Rica attributable to malaria that we could find was in 2009 when an Englishman who contracted malaria in Nigeria, had a relapse that he did not recognize and have treated until it was too late. There have been no deaths attributed to malaria since.
The CDC website continues to hold an advisory for the Limon Province. This does not mean that the risk from malaria in the province of Limon is greater than before but rather that the CDC has recognized, albeit belatedly, that there is negligible risk from malaria in the other provinces of Costa Rica.
As far as medication goes, there is general agreement that Malarone has much fewer side effects and is just as effective as the older drugs such as chloroquin. Deciding whether or not you take the pills is essentially a risk/benefit analysis. In your position we would not take them, but if not doing so is going to mean that you or your traveling companion is going to be at all worried about the risk, then peace of mind might well be sufficient reason to take them.
This all said, finally you have to make your own decision about whether to use malaria prophylaxis or not.(The CDC is not the only ones who cover their backs).