Watchdog database size
Make sure that cron is running, that should clean that out the watchdog table regularly.

http://api.drupal.org/api/drupal/modules--dblog--dblog.module/function/dblog_cron/6

Drupal has a setting that controls how many rows should be kept, which you can configure at:

Drupal 6: /admin/settings/logging/dblog

Drupal 7: /admin/config/development/logging

Additionally, you should check what kind of logs you have in that table. Maybe a module or something is causing a lot of notices which are all logged there (And considerable slow down your site!)

You can of course simply truncate the table, but you should first figure out why it's not getting cleaned and what is filling it up like that. How many rows are there?