There are lot of reasons why you would have water in the trunk of your CRX. One of them is the sunroof drain hoses. The Si models came with the sunroof. There are total of four drain hoses from the sunroof. One on each corner. Two are routed through the a-pillar, ends up somewhere inside the front fenders, and drains out behind the front wheels. So far so good. The two rear hoses are routed along the c-pillar (along the lines of the rear hatch) through the trunk area and drains out behind the rear wheels. Pretty straight forward set-up except that the rear hoses are NOT one continuous hose.

I have no idea why some dude thought it was a good idea to have two connecting hoses and have them meet inside the trunk area right behind the wheel well. The upper hose is thinner than the lower so that its end is inserted into the lower hose to create the continuous drain. But this is where they come apart because they didn’t make the hoses long enough! Few more inches of upper hose would have kept them securely connected. Now they almost butt against each other end to end. I’m sure the hoses have shrunk over the years, but the dude should have thought about that in the beginning.

What happens once they come apart? The water no longer drains out under the car but sits in your trunk behind the wheel wells. I believe this also works to accelerate the famous Honda “rear wheel arch rust”. Honda is usually good at little details but this is one that’s utterly stupid. So if your CRX came with a factory sunroof, check each corner of your trunk behind the rear wheel well. Make sure those two hoses are tightly connected. And even if they are connected now, I’d duct tape them real good.