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If the heater matrix was leaking you would be losing coolant from the header/filler tank. If pour water directly at the air inlet of course water will flow inside. When water enters the scuttle area it should be able to drain away fast enough to prevent any water building up high enough so it can't flow into the air duct. Have you been able to locate the drain holes (usually one each corner of the scuttle). Some have a one way valve rubber flap which tends to jam. Ensure these drains are properly cleared -if necessary rod them with a piece of soft wire and give them a good flush out with the hose.
Currently in madnoel10's garage:
Honda Civic 1.4l