The solution to your question is to understand how aperture, shutter speed, focal length and ISO work together.
Aperture, Shutter speed and ISO combined determines the exposure. Typically you will want your reef pictures to be properly exposed (not too dark not too light). Shutter and aperture are reciprocal - i.e. the faster the shutter (shorter exposure), the larger the aperture has to be (lens opening) in order to gather the same amount of light.
Aperture furthermore determines DOF (Depth of Field) - what is in focus and what not. Shutter speed determines whether a moving object is frozen in place (fast shutter) or blurry (slow shutter). Obviously for stationary things you can use a slower shutter - the faster the subject moves the faster the shutter to freeze the motion.
ISO defines the sensitivity of the sensor. The lower the ISO, the less noise in the image but the more sensitive i.e. more light is gathered. Doubling the shutter speed halves the exposure unless you either double the aperture or ISO. ISO does not affect DOF.
Focal length implicitly determines your perspective (it does not in itself change perspective, but it usually causes you to move forward /backwards for the composition thus affecting perspective). It also determines the FoV (Field of View) - what is in the picture and what not. Long focal lenghts causes a small area of your subject to fill the frame, and wider focal lengths causes more of the subject to be visible. Note that focal length affects apparent DOF - the longer the focal length the less apparent DOF you'll have, and vice versa. I say "apparent" since it does not truly affect DOF, just our perception of it.
Based on this, you should be ready to understand that taking a photo of a swimming fish will typically require a fast shutter and large aperture and high ISO assuming a side profile so no large DOF is required.
Taking a closeup of a polyp typically requires a slower shutter provided the flow is low, smaller aperture to get more DOF, large ISO to get enough exposure and long focal length to get up close.