It's not clear from your question if you want to run Integration tests (Front end + back end) or Unit Tests against you Database layer.
If you need a tool that allows you to write Integration tests, you should definitively look at Selenium.
With Selenium you can generate functional tests by simply navigating your web site (JSP pages) and asserting that stuff on the page exists or it's equal to some values.
Selenium comes with a Firefox plugin that will basically generate the code for you. You can replay the test in the browser or export them as Java code and make them part of your test suite. Selenium is an invaluable tool.
The drawback of using a tool like Selenium is that your application need to be deployed somewhere before you can run your test suite. This may be a limitation if you plan to run automated tests generated using Selenium.
If you are only interested in testing your database access code (DAO, Data Access Layer) DBUnit is the perfect tool.
Generally, DBUnit is used to initialize the database tables before testing and, less often, to run assertions on the database content. DBUnit uses an XML based format to represent the data that will be inserted into the database.
The XML files containing the data to pre-populate the db are normally triggered by a build script (Ant, Maven, etc.) or directly in your unit test code.
I have used both approaches, it really depends on how your code is structured and how you access the database (Hibernate, Spring+Hibernate, JDBC...).
If your database is not too big, I'd recommend you populate it just before running your test suite. Alternatively, you can populate only the tables that you are interested in testing prior to every test.
Here is a link to Unitils, that is an additional library that can be used on top of DBUnit to simplify the database testing strategy. I think it can be used as a reference to get you started:
http://www.unitils.org/tutorial.html#Database_testing
Here is anoter link (quite old, 2004) showing the basic mechanics of DBUnit:
http://onjava.com/pub/a/onjava/2004/01/21/dbunit.html