Depending on the collection area and the sailing, salt can be a primary problem. Spray falls and dries, layer after layer, until the decks hold enough salt to foul a considerable flow of water. The solution? Wash the deck with seawater before the rain comes. Squeegee off as much as practical or towel dry, and common sense dictates this is best done when at sea and must be done away from red tides. We tested the run-off from the top after scrubbing with seawater, allowing to dry, and then spraying with tap water equivalent to 1/10-inch of rain. In addition to taste, seawater contains significant sulfate levels, which combined with bacteria in the tank under anaerobic conditions, can lead to sulfurous water; sailors notice this when a seawater flush is used for the head, but allowed to become stagnant for a few days; the first flush will smell.
So, yes, if water is collected from a dirty, salt encrusted deck, it will be unpalatable, contain pollutants, and no filter will help. If you collect from the deck, at least wash it with seawater. If you need to collect while underway, keep a close eye on spray. Another reason to collect from raised surfaces like awnings, biminis, and hard-tops.