I mentioned sun, time and angles for best blue water photography earlier. Next important factor for clarity is correct timing in regard to tides. Hence some basic knowledge of tide tables is necessary for best clear blue water photography.
During high tide the water in lagoons and coastal water is clearer and thus the blue cleaner in shallow water and lagoons. While during low tide hours the water is substantially more turbid and saturated with more dirt particles.
SCUBA divers know such rules of course most beautiful dives are best planned during high tide. Same applies for blue water photographer wishing clearest waters for best brilliant color results.