Main Sanctum Sanctorum: The temple is located a little away from the banks of the Manimalayar (river) at Thiruvalla. The Swayambhu Shiva Lingam is dedicated to the inside of a square Sanctum Sanctorum. The presiding deity of the temple is Lord Shiva as Thiruvatta Thevar, facing East. The self-glorious Shiva lingam is placed a little lower inside the sanctum. Because of the low statue of the temple, the sacred statues of the valiya balikallu (great sacrifice stone) and the Nirmalayadhari are depicted. The Ganapati is located in the south east corner of the main shrine. The walls of the main shrine in rectangular shape is made of granite and the top is covered with copper plate.
Nalambalam: Nalambalam of the temple is very wide quadrangle. The walls of nalambalam is made of limestone. There are two shrines inside the Nalambalam. The main shrine has a self-contained Shiva lingam and a very tall rectangular shrine to the south of it. There are two shrines inside the nalamabalam. The main shrine has a swayambhoo Shiva linga and second shrine has a big shiva linga installed separately.[9] During the year, the main sanctum sanctorum sinks with rain water and the Arattu abhishekam is performed on the day of Lord Shiva (Thiruvata Thevar.) When the main Shiva Linga sinks, the routine pooja of temple is placed in the south shrine of Shiva linga.
Mandapom: On the east side is a main shrine a namaskara mandapom built with a rectangular shape. In the sanctum and the mandapam also covered with copper plate. The nambalam and its adjoining balikkal mandapam are built to reflect kerala / dravidian architecture. Similarly, stone walls are placed on the nalambalam walls of the temple.