The present temple is built in Kerala Temple Architecture style, which is almost common in all temples in Kerala.
A rectangular wall around the temple, called kshetra-matilluka pierced by the gateways, encloses all the temples within the temple. The metal plated flag-post (dvaja sthambha) is located axial to the temple tower leading to the central sanctum and there is a dipasthambha, which is the light post.
Chuttuambalam is the outer pavilion within the temple walls. The central temple and the associated hall is located in a rectangular structure called nalambalam, which has pillared halls and corridors.
Between the entrance of nalambalam to the sanctum, there is a raised square platform called namaskara mandapa which has a pyramidal roof. Thevrapura, the kitchen used to cook offering to the Navamukunda is located on the left of namaskara mandapa from the entrance. Balithara is an altar is used for making ritualistic offering to demi-gods and the festive deities.
The central temple called sri kovil houses the idol of the Navamukunda. It is on an elevated platform with a single door reached through a flight of five steps. Either sides of the doors have images of guardian deities called dvarapalakas. As per Kerala rituals, only the main priest called tantri and the second priest called melsanti alone can enter the sri kovil.
The central temple has a square plan with the base built of granite, superstructure built of laterite and conical roof made of terracotta tile supported from inside by a wooden structure. The roof projects in two levels to protect the inner structure from heavy rains during monsoon. The roof of the temple and some of the pillars have lavish wood and stucco carvings depicting various stories of epics, Ramayana and Mahabharata.
The outer walls around the sanctum have a series of wooden frames housing an array of lamps, which are lit during festive occasions.
River bank where austerities are performed for forefathers
The idol of Navamukunda is portrayed only from above the knee, the rest of the idol being concealed within the ground. There is believed to be a bottomless unexplored pit behind the idol in the sanctum. The idol of the Navamukunda is 6 ft (1.8 m) tall, and is made of stone and covered with pancha loha. The idol is in a standing posture, with four hands carrying Panchajanya conch, lotus flower, Kaumodaki mace and the terrible Sudarshana discus. The idol is facing east.
Goddess Lakshmi has a separate sri kovil in the Tirunavaya Temple. The sri kovil is in the north-west of the nalambalam, to the left of Navamukunda, and the idol is facing east. The idol only have two hands, with varadabhaya
Pitru Tharpanam or Thithi or Pinda pradhanam
This temple is famous for pitru tharpanam. Like most of the temples in Kerala, One has to pay charges at the ticket counter which is hardly less than 100 rupees, And dip in the river(clothes the male needs to wear is mundu or dhoti or veshti) and in the wet clothes offer the tharpanam. All the ritual pooja items will be provided by the temple. After the ritual is complete, the wet clothes have to be changed. The temple strictly does not allow pants or other non Indian wear. Strictly men have to be in dhoti and their shirts removed.