How to split limited time between the two World Heritage sites.
If you only have three days, reef weather forecasts matter more than rainforest ones — book the outer reef trip for whichever day has the calmest forecast and build the Daintree day around it. Reef trips are also more schedule-dependent (fixed boat departure times), while the Daintree is flexible enough to shift a day if needed.
A full Daintree day realistically means an early start — it's a two-hour drive each way from Cairns, so an overnight in Cape Tribulation is worth considering if you want more than a rushed look before driving back.