From Pembroke bus to Ċirkewwa, walk to Cirkewwa, then ferry to Blue Lagoon. 2 h 6€.
How to get from Valletta to Comino?
There is no direct connection from Valletta to Comino. However, you can take the bus to Ċirkewwa, take the walk to Cirkewwa, then take the ferry to Blue Lagoon.