im sure theres a few things it could be.. but on mine.. the back left corner sits up and doesnt seal.. and usually that means theres something wrong with the cable assembly... not pulling the sunroof all the way down and locking it in place. Honda Automotive Parts go to that linke and look at number 14... and youll see what im talking about. im personally going to buy the sunroof plug kit.. ive always had leaky sunroofs.. not much of a fan of them myself personally. hope this helps.
Mine has the same problem with the sunroof and its a worn out lift-up link. Go here and download the manual for your crx. It has details on how to change it if you need to. Mine will close fine as long as I don't open it all the way to the backstop so I haven't bothered changing it. Free Downloads of Civic Wiring Diagrams and Schematics from HELMS Manuals - At Spoonhonda.com
good luck
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