Water leak passenger and driver side, wet carpet

Our 2009 Sienna LE passenger side and driver side carpet are both soaked - with the passenger side wetter.

This has happened twice already - San Francisco bay area gets rain mostly in winter months.
The first time, I thought it must have been my fault: not closing the window.
But this time, I am pretty sure it is not the window.

-The leak is water, no sweet smell etc. The heater is working.
-We hardly used A/C, heater. Checked A/C drainage pipe from below, it was not blocked.
-There is no moonroof
-Windshield is factory (it is a 2009 model after all)

Is this kind of problem covered by warranty?

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For the convenience of search, here are threads I have found regarding wet carpet issue:
* Water leaking into passenger side => http://siennachat.com/forum/index.php/topic,301.0.html
* Front carpet wet => http://siennachat.com/forum/index.php/topic,1247.0.html
* Sienna Front water leak => http://siennachat.com/forum/index.php/topic,761.0.html