A solar cover can heat your water by:
Getting hot and conduction of heat to the water.
Acting like a greenhouse and preventing heat from leaving (insulation)
Acting like a greenhouse and allowing sunlight to pass through and heat the water directly.

A clear cover does all three, but the first it does least effectively.

An opaque cover does the first two, but not the third.

A transparent blue cover does all three, the first slightly more effectively than a clear cover, but the third seems to be less effective than a clear cover.

I've had all three and prefer a clear cover, heavy enough to give good insulation.