seaQuest DSV is a real-time simulator/strategy game depiction of the seaQuest DSV television series for the Super Nintendo Entertainment System and Mega Drive/Genesis. The player takes the role of the captain of the submarine seaQuest DSV 4600, and is tasked with carrying out a series of missions in a series of levels, divided up as "ocean quadrants". There is a Game Boy game as well, although completely different compared to the 16-bit console versions.

The game is divided into two parts; one in which you control the seaQuest in an isometric perspective overworld and are able to buy equipment and weapons and travel the ocean quadrant, and the actual horizontal scrolling shooter style missions, in which you are to achieve various objectives using a complement of mini-subs, robots, and even a trained dolphin wearing an aqua-lung. Some of the missions are simplistic and require you to make use of only one of the seaQuest's vessels, others have you make use of several of them in succession. For example, there's a mission in the first ocean quadrants where you have to rescue the crew of an exploration vessel trapped in a caved-in underwater cave, and have to use armed subs to clear several cave-ins before you can bring in the only mini-sub you have that's equipped to rescue personnel from other subs. The missions also typically involve combat between your mini-subs and the units of pirates, eco-terrorists, and other foes, but also more often than not require you to perform some sort of non-combat task such as the aforementioned rescue operation.

The other part of the game is the overworld where the player controls the seaQuest herself. These areas give you access to several menus in which you can replace lost equipment, buy new weapons for the seaQuest, and read up on the various missions you will receive while in your quadrant. While traveling your quadrant, you will also come across minefields, automated torpedo launchers and hostile submarines, many of which you need to destroy in order to achieve missions you are assigned in their area. For example, there's a mission in which you are to seal the leaks in an oil tanker sunk by ecological terrorists. In addition to accomplish this objective with your mini-subs, you need to not only complete the mission itself, but also to use the seaQuest herself to sink every terrorist submarine near the oil tanker wreck.

The game features a currency system, and awards you money for destroying enemy targets and completing objectives. The player can also lose money for destroying underwater settlements and killing animals present in some missions. Money is spent on weapons, countermeasures and mines for your seaQuest submarine, as well as replacements for lost vessels in missions. You don't need to spend money on repairs, though, as the seaQuest and her complement subs repair themselves over time.