Boat Troop personnel are specialists in "sub aqua and surface swimming skills and the techniques required to use small surface craft and semi-submersibles, members of Boat Troop have skills similar to those of the commandos of the Special Boat Squadron (SBS). Special Air Service soldiers train with both open- and closed-circuit scuba systems, the latter preventing tell-tale bubbles from reaching the surface to alert a watchful enemy; silent klepper two-man canoes; high speed Rigid Raider assault craft; and a variety of military inflatables and more conventional landing craft." (Fighting Skills of the S.A.S. p.172-173)

Boat Troop saw a lot of action during the Falklands campaign and I would expect them to be operating more recently in the Iraq war as many of Iraq's major cities lie on the Euphrates and Tigris rivers.
Boat Troop's missions can be quite varied. From planting explosives on enemy shipping, recon on enemy ships, to assaulting or reconnoitring targets that can be accessed from the sea or inland waterways. Their versatility means they can land in nearly all but the most extremes of weather which gives them an element of surprise and cover as they are difficult to spot, particularly when inserted at night and can slip in under the enemy radar.