Tomcat Guice/JDBC Memory Leak

I just dealt with this problem myself. Contrary to some other answers, I do not recommend issuing the t.stop() command. This method has been deprecated, and for good reason. Reference Oracle's reasons for doing this.

However there is a solution for removing this error without needing to resort to t.stop()...

You can use most of the code @Oso provided, just replace the following section

Set<Thread> threadSet = Thread.getAllStackTraces().keySet();
Thread[] threadArray = threadSet.toArray(new Thread[threadSet.size()]);
for(Thread t:threadArray) {
    if(t.getName().contains("Abandoned connection cleanup thread")) {
        synchronized(t) {
            t.stop(); //don't complain, it works
        }
    }
}

Replace it using the following method provided by the MySQL driver:

try {
    AbandonedConnectionCleanupThread.shutdown();
} catch (InterruptedException e) {
    logger.warn("SEVERE problem cleaning up: " + e.getMessage());
    e.printStackTrace();
}

This should properly shutdown the thread, and the error should go away.

I've had the same issue, and as Jeff says, the "don't worry about it approach" was not the way to go.

I did a ServletContextListener that stops the hung thread when the context is being closed, and then registered such ContextListener on the web.xml file.

I already know that stopping a thread is not an elegant way to deal with them, but otherwise the server keeps on crashing after two or three deploys (it is not always possible to restart the app server).

The class I created is:

public class ContextFinalizer implements ServletContextListener {

    private static final Logger LOGGER = LoggerFactory.getLogger(ContextFinalizer.class);

    @Override
    public void contextInitialized(ServletContextEvent sce) {
    }

    @Override
    public void contextDestroyed(ServletContextEvent sce) {
        Enumeration<Driver> drivers = DriverManager.getDrivers();
        Driver d = null;
        while(drivers.hasMoreElements()) {
            try {
                d = drivers.nextElement();
                DriverManager.deregisterDriver(d);
                LOGGER.warn(String.format("Driver %s deregistered", d));
            } catch (SQLException ex) {
                LOGGER.warn(String.format("Error deregistering driver %s", d), ex);
            }
        }
        Set<Thread> threadSet = Thread.getAllStackTraces().keySet();
        Thread[] threadArray = threadSet.toArray(new Thread[threadSet.size()]);
        for(Thread t:threadArray) {
            if(t.getName().contains("Abandoned connection cleanup thread")) {
                synchronized(t) {
                    t.stop(); //don't complain, it works
                }
            }
        }
    }

}

After creating the class, then register it on the web.xml file:

<web-app...
    <listener>
        <listener-class>path.to.ContextFinalizer</listener-class>
    </listener>
</web-app>