Ocean4you provide a wide range of tours from their base in Tavira.
Sabina Boat Tours offer a wide range of water bvased tours from theit base in Olhão. Have a look at their website for more information.
Sequatours offer an excelent choice of water based tours from their bases in Tavira and Cabanas. In addition they also provide a water teaxi service for these areas. More information can be found on their website.
Passeios Ria Formosa provide water based tours operating along the coast in the East Algarve in Olhão. Fuzeta and Santa Luzia.
Formosamar tours proving a wide range of local tours out of Faro