The dry season runs from November to April and is the best time to visit. Temperatures sit around 25–28°C, humidity is manageable, and the water is calm and clear. December through February is peak tourist season — comfortable to be outside all day, but prices are higher and the ferries from Cancún carry more visitors.
May to October is the wet season. Temperatures climb and humidity rises sharply. Rain usually comes in afternoon downpours rather than all-day grey — mornings are often perfectly clear. The upside is lower prices, far fewer crowds, and the whale shark season. From May to September, aggregations of whale sharks gather in the warm waters north of the island to feed on fish spawn. Isla Mujeres is one of the best places in the world to swim with them; several operators run regulated tours from the island.
September and October are peak hurricane season. The Yucatán is periodically hit by serious storms during these months. Most years pass without incident at this scale, but it is worth checking weather forecasts and having flexible travel arrangements if you visit in autumn. The upside of off-season pricing and empty beaches is real, but so is the risk.
The lobster season runs from June through February, which makes the heart of the wet season also the best time to eat well.