I am not the most practical of persons. Nevertheless, if i had a build-up of water in my shed due to a leak, I would find where the water is deepest and drill a small (5mm?) hole there, making sure that below the floor at that point, there is nothing that will stop the water draining away. I would use a cordless drill taking the precautions outlined in other replies. I would then seal the wood and plug the hole just in case the exercise had to be repeated after another leak. That is what I would do but I am hardly what you would call a DIY buff.
Disagree JohnD. Am talking from experience. Had the same problem, did as I advised the poster to do and the water drained away. Plugged the hole with an old washing-up liquid cap and it's still in place after 4 years.