The MySQL JDBC (v3.1.10) drivers included with ADS work across all versions of MySQL from 3.x to 4.1. MySQL server releases are very frequent, and may sometimes require updating the JDBC driver.
You may locate the latest MySQL JDBC drivers at the following location ...

Vendor: MySQL
Driver URL: http://www.mysql.com/products/connector/j/

To update the ADS JDBC drivers you need to overwrite the ADS mysql.jar file. Below is a listing of the Aqua Data Studio library directory [ADS_HOME]\lib\drivers\ ...

Driver Location (Windows/Linux):

[ADS_INSTALL]\lib\drivers\mysql.jar

Driver Location (OSX):

/Aqua Data Studio/Contents/Resources/Java/drivers/mysql.jar

C:\Program Files\Aqua Data Studio 7.0 - 32bit\lib\drivers>dir
 Volume in drive C has no label.
 Volume Serial Number is AC70-D62C

 Directory of C:\Program Files\Aqua Data Studio 7.0 - 32bit\lib\drivers

05/30/2008  08:48 AM    dir          .
05/30/2008  08:48 AM    dir          ..
03/20/2008  10:05 PM         1,146,367 db2java.jar
03/20/2008  10:05 PM         1,973,658 db2jcc.jar
03/20/2008  10:05 PM             1,015 db2jcc_license_cu.jar
03/20/2008  10:05 PM         2,343,388 derby.jar
03/20/2008  10:05 PM           489,802 derbyclient.jar
04/05/2008  01:15 PM           218,162 derbynet.jar
03/20/2008  10:05 PM           685,631 ifxjdbc.jar
03/20/2008  10:05 PM           529,560 jconnect60.jar
03/20/2008  10:05 PM         4,301,866 jt400.jar
03/20/2008  10:05 PM           554,589 jtds-src.jar
05/06/2008  09:46 PM           297,610 jtds.jar
03/20/2008  10:05 PM           655,034 mysql-src.jar
03/20/2008  10:05 PM           676,693 mysql.jar
04/16/2008  09:29 AM         1,645,114 nlscharset12.jar
04/16/2008  09:29 AM         1,545,954 oracle.jar
03/20/2008  10:05 PM           415,542 postgresql.jar
03/20/2008  10:05 PM           286,771 util400.jar
03/20/2008  10:05 PM           139,148 xdb.jar
03/20/2008  10:05 PM           839,982 xmlparserv2.jar
              19 File(s)     18,745,886 bytes
               2 Dir(s)  17,642,438,656 bytes free

The Java class path for the drivers are already configured for ADS in the datastudio.cfg for launching ADS with datastudio.exe and in datastudio.bat/.sh and datastudio-bundled.bat/.sh for launching ADS from the command line. The contents of the file are as follows ...

C:\Program Files\Aqua Data Studio 6.5>type datastudio.cfg

.

.\jre\bin\javaw.exe

-Dsun.swing.enableImprovedDragGesture -Xmx256M -cp ".\lib\ads.jar;
.\lib\aqua-lib.jar;
.\lib\aspc.jar;
.\lib\aqua2.jar;
.\lib\oracle.jar;
.\lib\nlscharset12.jar;
.\lib\jtds.jar;
.\lib\derby.jar;
.\lib\derbyclient.jar;
.\lib\mysql.jar;
.\lib\postgresql.jar;
.\lib\db2java.jar;
.\lib\db2jcc.jar;
.\lib\db2jcc_license_cu.jar;
.\lib\ifxjdbc.jar;
.\lib\jconnect55.jar;
.\lib\jconnect60.jar;
.\lib\xmlparserv2.jar;
.\lib\xdb.jar;
.\lib\activation.jar;
.\lib\jaxb1-impl.jar;
.\lib\jaxb-api.jar;
.\lib\jaxb-impl.jar;
.\lib\jaxb-xjc.jar;
.\lib\jsr173_1.0_api.jar;
.\lib\stringtemplate.jar;
.\lib\jide-action.jar;
.\lib\jide-beaninfo.jar;
.\lib\jide-common.jar;
.\lib\jide-components.jar;
.\lib\jide-dialogs.jar;
.\lib\jide-dock.jar;
.\lib\jide-grids.jar;
.\lib\jide-pivot.jar;
.\lib\jide-shortcut.jar" com.aquafold.datastudio.DataStudio

C:\Program Files\Aqua Data Studio 6.5>type datastudio.bat
SET ADS_PATH=
SET ADS_PATH=%ADS_PATH%;.\lib\oracle.jar
SET ADS_PATH=%ADS_PATH%;.\lib\nlscharset12.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jtds.jar
SET ADS_PATH=%ADS_PATH%;.\lib\derby.jar
SET ADS_PATH=%ADS_PATH%;.\lib\derbyclient.jar
SET ADS_PATH=%ADS_PATH%;.\lib\mysql.jar
SET ADS_PATH=%ADS_PATH%;.\lib\postgresql.jar
SET ADS_PATH=%ADS_PATH%;.\lib\db2jcc.jar
SET ADS_PATH=%ADS_PATH%;.\lib\db2jcc_license_cu.jar
SET ADS_PATH=%ADS_PATH%;.\lib\db2java.jar
SET ADS_PATH=%ADS_PATH%;.\lib\ifxjdbc.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jconnect55.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jconnect60.jar
SET ADS_PATH=%ADS_PATH%;.\lib\aqua-lib.jar
SET ADS_PATH=%ADS_PATH%;.\lib\aqua2.jar
SET ADS_PATH=%ADS_PATH%;.\lib\xmlparserv2.jar
SET ADS_PATH=%ADS_PATH%;.\lib\xdb.jar

SET ADS_PATH=%ADS_PATH%;.\lib\activation.jar
SET ADS_PATH=%ADS_PATH%;.\lib\aspc.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jaxb1-impl.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jaxb-api.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jaxb-impl.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jaxb-xjc.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jsr173_1.0_api.jar
SET ADS_PATH=%ADS_PATH%;.\lib\stringtemplate.jar

SET ADS_PATH=%ADS_PATH%;.\lib\jide-action.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-beaninfo.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-common.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-components.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-dialogs.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-dock.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-grids.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-pivot.jar
SET ADS_PATH=%ADS_PATH%;.\lib\jide-shortcut.jar