There are visible clues. Landforms at the shoreline usually continue their shape and direction under water. A steep cliff above the surface implies a steep wall below. A canyon leading down to the shore probably continues under water, though it may be partially filled with sand. An offshore rock that's steep on one side and gently sloping on the other probably has the same shape below the surface.
Water color indicates deep or shallow, sand or grass.
Kelp beds will be visible from above. Take time with this, so the image has a chance to fix itself on your memory. Sketching the site on your slate will help you remember it, even if you never refer to the sketch. Now look for directional clues that will be visible from under water. Fairly small wave fronts will be visible from below.