Muthirikinaru is the sacred well located in the north-western corner of Swamithoppu village. This is the famous theertha of the temple. Muthirikinaru means the well on which the Lord had affixed His seal.
Before and during the period of Lord Vaikuntar, this part of the subcontinent was under the grip of feudalism, casteism and untouchability. There were separate wells and tanks for each caste, and people from the other caste were not allowed to draw out water from those wells. Vaikuntar wanted to stop this evil practice. So he established this sacred well at Swamithoppu. It was the first well in this part of the country where people could use water freely irrespective of their caste.

People from far and wide and of different castes congregated there to draw out water for bathing and drinking. Lord Vaikuntar used the holy water from the well and the holy mud to cure the people of their illness. When the caste Hindus heard of this, they became jealous; so, they put poison into the well.
Lord Vaikuntar concentrated the poison into a sivalinga and the sivalinga remained inside the well. People, hearing about the poisoning reported it to Vaikuntar and requested Him to save them. Vaikuntar informed the devotees that the water in the well was non-poisonous. People who had faith in his words drank and bathed in the well and were totally safe. Those who had no belief in his words and had drunk the water became unconscious. People rushed to the Lord and narrated the incident. Lord asked them to sprinkle the holy water on those who were unconscious. They got up as if from sleep.

Even today the well is too crowded to bathe. People drink this water as patham. Pathapaduthuthal is a Tamil word meaning processing. It is believed that the holy water from this well will process one for the life of Dharmayuka. It is believed that lunatics and patients having no cure even after Prolonged medical Treatment, stay in the temple, take bath in muthirikinaru and get cured.

The Gurus start their daily routine only after bathing in the well. Lord Vaikuntar is carried to muthirikinaru on a horse vahana on the eighth day of the festival. It is believed that the God hunts kali. The ceremonial hunting of kali done with a bow and arrow. Here, thousands of people assemble to drink the holy patham. Patham viduthal is the word used by the devotees for bathing in Muthirikinaru. There is a heavy rush to take bath in the well on the first Sunday of Tamil months.

On September 17, 1994, the first Sunday of Puratasi, there happened a miracle at the well. Some miscreants immersed 5 kg packet of Phorate, a highly poisonous chemical, into the well. There was a smell of this chemical everywhere around the well. Some advised the devotees not to bathe in the well. But, nobody heeded it; thousands of people bathed and drank the water. Even six month old babies were bathed here. But the poisonous chemical did not harm anyone.

The empty packet of the chemical was later retrieved and destroyed. Ayya Vaikuntar protected his devotees from the poison. It was a great miracle and all those who witnessed this, praised Vaikuntar chanting ayya siva siva arakara arakara. Arul nool, one of the two holy books, advises everybody to do dharma near this well. There is an annadharmasala, a feeding house, near the well.

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