Panchathirtha is situated towards the southern side of the Thirunelly temple. The word Pancha means five and thirtha represents the rivers. As per the ancient traditions Panchathirtha is a large, splendid lake encompassing the Sankha, Chakra, Badma, Gatha and Sreepaada tirthas. It is believed that these five met at a point and hence acquired this name.

Today, this pond is merely a puddle, but it yet retains the rock with the imprint of the Sreepada on it. It is believed that Lord Vishnu stood on this rock to give instructions to Lord Brahma. Recently, Panchathirtha goes very dry during the summers.