check the seal on the windshield and the back window there are some small holes that are supposed to drain the water out from under the window seal but if you have good seals it shouldnt really be getting under there.
... also your 69 should have a fresh air vent in the front hood, there is a fresh air box that should be under that vent. That box has a drain in the bottom with a hose that should go through a hole right behind the gas tank. if the box is missing or the drain stopped up or the hose disconnected or trashed it can drain water into the inside... especially if the hole has rusted through (my 68 did that). Also if the wing window seals are bad, water can drip down the door panels and end up on the floor, especially if you have them open during a rain storm. Finally the stock anrenna hole seal, if bad or missing, will leak water right down on to your heater channel and rust it into swiss cheese- (like my 69)
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There are a couple other possibilities, but best thing to do is sit in it on a dry day and have someone hose it down real good : )
You didnt mention if it got wet if you WERE NOT driving it, which leads to a few more places like body to pan seal, front tunnel opening plate/ seal
Regardless find and stop those leaks or you might be doing a heater channel/floor pan restoration one day! BTW you didnt mention what kind of shape the car is in. is it a rust bucket, or a mint 69 with only a handful of miles on it? It does matter. If the floor is a flintstone mobile water splashing up through all the rust holes will get the carpets all wet when driving in rain.... so see it does matter. Post some pics if possible.