You can install QGIS3 and QSWAT3 at the same time as QGIS2 and QSWAT2. If you are in the middle of a project you are strongly advised to complete it before upgrading. While we have tried to ensure that QSWAT3 is free from bugs, it is new code. The change to QGIS3 is being made because QGIS2 is no longer supported. Warning: QSWAT3 and QSWAT3_64 are functionally equivalent to QSWAT. Don't do that! Back out without uninstalling Office and check these release notes again. If you make a mistake and there is a mismatch between your version of Microsoft Office and the database engine you choose, you will get a warning that you need to uninstall Microsoft Office. You should also download and install Microsoft Access Database Engine Redistributable 2016, and choose the 64 bit version (called accessdatabaseengine_X64.exe). If you have a 64 bit machine with no Microsoft Office, or with a 64 bit version of Microsoft Office, you you need a 64 bit version of QGIS 3 (currently you should choose 3.10) and QSWAT3_64.
You should also download and install Microsoft Access Database Engine Redistributable 2016, and choose the 32 bit version (called accessdatabaseengine.exe). If you have a 32 bit machine or you have a 32 bit version of Microsoft Office on a 64 bit machine, you need a 32 bit version of QGIS 3 (currently you should choose 3.10) and QSWAT3. You choose between QSWAT3 and QSWAT3_64 based primarily not on what machine you have but on whether you have a 32 bit version of Microsoft Office, or a 64 bit, or don't have Microsoft Office at all. Existing users of QSWAT and ArcSWAT can continue to use their current installation of the SWAT Editor and the SWAT executable with QSWAT3 and QSWAT3_64. QSWAT3 and QSWAT3_64 are 32 bit and 64 bit ports of QSWAT to QGIS 3. Release Notes for QSWAT3 and QSWAT3_64 version 1.1
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