The temple is oriented to the east and features two towers along with two courtyards, complemented by a sacred pond at its forefront. The five-tiered tower showcases exquisite sculptures, and upon entering through its gate, visitors encounter a flagpole and an altar. In the outer courtyard's north-east corner lies a wedding hall and the sannidhi of Goddess Oppilla Nayaki, which faces south and depicts Her in a standing position with four arms. The northern outer courtyard houses the sannidhi of Sage Agasthiya, and is directly opposite the ‘Agasthiya theertham,’ a unique water body that always has water, no matter the season. Entering through the gate of the three-tiered second tower leads to the inner courtyard, where the sannidhi of Somaskandar and Chandrasekhar are located in the southeast. The southern courtyard features Sapthakanniya, Dakshinamoorthy, and Ayyanar, while a dedicated sannidhi for Valampuri Vinayaka is found in the corner. Additionally, the western courtyard contains a separate sannidhi for Muruga alongside Deivanai, and on the southern side, there is a sannidhi for Varadaraja Perumal accompanied by Ubhaya Nachiyar.

In the sanctum of Nedungalam, the deity adopts a unique posture, allowing Shakthi to take center stage by presenting the left side of his body as Artha-Nareeshwarar. Although the physical representation within the sanctum is primarily that of a Shiva linga, it is widely believed that both Shakthi and Shiva inhabit this sacred space, with Shakthi existing in a formless state referred to as 'Aroopam.' This duality is further emphasized by the presence of two vimanas, or towers, that adorn the sanctum, a feature that is notably rare and primarily found in only one other location, Kasi. The significance of Nedungalam is further enriched by its historical context, as it is said to be the site where Devi Parvathy undertook rigorous penance to attain the grace of Shiva.