Wrecks may pose a variety of unique hazards to divers. Wrecks are often snagged by fishing lines or nets and the structure may be fragile and break without notice. Penetration diving, where the diver enters a shipwreck is an advanced skill requiring special training and equipment. Many attractive or well preserved wrecks are in deeper water requiring deep diving precautions. It is essential that at least one cutting device be carried in the event that the diver is entangled with fishing lines or ropes and to have a spare light source in case the primary light fails. If penetrating a wreck, a guideline tied off before entering a wreck and run out inside the wreck is advisable. A guideline helps a wreck diver in finding the way out easier in case of low visibility due to stirred up sediments. For penetration diving, a greater reserve of breathing gas should be allowed for, to ensure there is sufficient to get out of the wreck. Most wreck divers use a minimum of the rule-of-thirds for gas management. This allows for 1/3 of the gas down and into the wreck, 1/3 for exit and ascent and 1/3 reserve. In addition, because of the potential fragility of the wreck, the likelihood of disturbing sediments or disturbing the many marine animals that take advantage of the artificial habitat offered by the wreck, extra care is required when moving and finning. Many divers are taught to use alternative finning methods such as frog kick when inside a wreck. Perfect buoyancy control is a must for diving in the environment of a wreck.

Many diver training organizations provide specialist wreck diver training courses, such as SDI, and PADI Wreck Diver, which divers are advised to take before wreck diving. Such courses typically teach skills such as air management and the proper use of guidelines and reels. Most recreational diving organizations teach divers only to penetrate to limit of the "light zone" or a maximum aggregate surface distance (depth + penetration) of 100 feet (whichever is the lesser). Other technical diving organizations, such as IANTD, TDI, and ANDI teach advanced wreck courses, that emphasize a higher level of training, experience and equipment and prepare divers for deeper levels of wreck penetration. The Nautical Archaeology Society in the UK, teaches awareness of underwater cultural heritage issues as well as practical diver and archaeological skills. Other organizations, such as the Artificial Reef Society of British Columbia (ARSBC) deliberately create artificial reefs to provide features for divers to explore, as well as substrates for marine life to thrive upon.