Is this in Emerald? If so you have to be quick, you take to long and the entrance will vanish. There's two different entrances on the route that the guy in the Weather Institute gives you - you'll need to find the one that is currently open. The main site gives pictures and the routes, go there for any other help.
Keep trying. Groudon's spots are easier to get to than Kyogre's in my opinion. but then again I suck with water Routes.