When we had our boat built the builder
encouraged us to put in rain water collection from day one and we are glad we did. Having the benefit of a builder
with much cruising boat sailing and design experience this is what we came up with.
On each side of the outer edge of the deck in the lowest point of the waterways beside the toe rail there is a deck drain that drops down inside the hull
and through a seacock to the sea (discharges underwater to avoid staining the topsides if drained above). All water that falls on any part of the boat apart from the cockpit
ends up there due to the falls on the deck and along the waterways.
The outer edge of the deck drain hole is in from the toerail an inch or so with a little fall from that to the inner edge of the toe rail - this serves to catch silt. The drain hole is also flush with the deck, so no lip around it. We have a punched toerail - the punched holes in it are just high enough so that the deck drain floods rather than the caught water going through the holes in the toerail.
A little under the deck inside the boat is a Tee fitted so the straight through has a ball valve immediately below it then hose to the seacock and the horizontal run has a ball valve on it and then goes to a water tank. These are also our tank fills - to fill a tank, either from a hose or when catching rain off the deck, one closes the valve under the Tee and opens the one off the horizontal run of the Tee to the tank (so there is no filler cap on deck - to fill the tanks from a hose one just pokes the hose into the deck drain). We have two fresh water tanks - the port drain goes to one tank and the starboard one to the other.
So under normal circumstances anything that goes down the deck drain goes to the sea, that including any malicious attempt by a weirdo to contaminate our water tanks as the tank fills are isolated by valves inside the boat (that is if they ever get to realise that the open deck drains serve as the tank fills). Having the run to the tanks horizontal off the Tee minimises the chance of collecting debris on the potable side of the Tee (whereas a Y would collect debris).
We carry 500 litres of water and in a down pour a tank will fill in tens of minutes (we are 40 foot) rather than in hours. Even in light rain it is surprising how much gets collected. We just give a few minutes first for the deck to wash clean of salt
We have never had a problem with contamination but obviously one doesn't do it if sea spray is also hitting the deck. We do not do any treating or filtering of the water and very couple of years I open the tanks up for inspection
but I have never found any silt or other material in them.
As some others have said there is nothing wrong with rainwater - many of us were bought up on it or still rely on it. Any important contamination will be from what one collects it on or allows to fall into it after collection. Think I would trust it more than bottled water myself.