Methods and gear used for diving from a boat diving are similar to shore diving or blue water hunting depending on the prey sought. Care must be taken with spearguns in the cramped confines of a small boat, and it is recommended that spear guns are never loaded on the boat.

Boat diving is practised worldwide. Hot spots include the northern islands of New Zealand (yellow tail kingfish), Gulf of Florida oil rigs (cobia, grouper) and the Great Barrier Reef (Wahoo, dog-tooth tuna). FADS are targeted worldwide, often specifically for mahi-mahi (dolphin fish). The deepwater fishing grounds off the Three Kings Islands in New Zealand are great for spearing marlin and people travel worldwide to try and spear this trophy fish.

Blue water hunting is the area of most interest to elite spear fishers, but has increased in popularity generally in recent years. It involves accessing usually very deep and clear water and trolling, chumming for large pelagic and game fish species such as marlin, tuna, mahi-mahi, Wahoo or giant Trevally. Blue water hunting is often conducted in drifts; the boat driver will drop one or more divers and allow them to drift in the current for up to several kilometres before collecting them. Blue water hunters can go for hours without seeing any fish, and without any ocean structure or a visible bottom the divers can experience sensory deprivation. It can be difficult to determine the true size of a solitary fish when sighted due to the lack of ocean structure for comparison. One technique to overcome this is to note the size of the fish's eye in relation to its body - large examples of their species will have a relatively smaller eye.

Notably, blue water hunters make use of breakaway rigs and large multi band wooden guns to catch and subdue their prey. If the prey is large and still has fight left after being subdued, a second gun can be used to provide a kill shot at a safe distance from the fish. This is acceptable to IBSRC and IUSA regulations as long as the spear fisher loads it himself in the water.

Blue water hunting is conducted worldwide, but notable hot spots include South Africa (yellow fin tuna) and the South Pacific (dog-tooth snapper). Blue water pioneers like Jack Prodanavich and Hal Lewis of San Diego were some of the first to go after large species of fast moving fish like Tuna.