It is believed that thousands of years ago the entire area now known, as Irinjalakuda was a dense forest a number of Rishis under Kulipini Maharshi were engaged in an incessant Yagna offering severe penance to please Maha Vishnu. Ultimately pleased at the intensity and sincerity of their devotion, the Lord appeared before them and offered to satisfy their wish. All they wanted was his eternal presence at the place. The Lord readily agreed.The Rishis now prayed to Deva Ganga to bless the sacred Yagabhoomi with her presence. As the springs of River Ganga fountained up and inundated the area the Rishis immersed themselves in the sacred waters and became one with the Lord.
The presence of Ganga is believed to continue in the Kulipini Theertham named after the chief of Rishis. This tank on the Northern side is believed to be as sacred as Sanctum Sanctorum. Water snakes, frogs etc. commonly found in most temple tanks are totally absent here. Only fish grow freely and feeding them is considered to be of special merit. Water for preparation of Nivedyam is taken form this tank only. Archakas after bath at the outside pond have to take a dip in Kulipini Theertham before entering Sanctum Sanctorum.
The temple itself was not built immediately after the incident narrated above. The place was not inhabited for many hundred years probably. The folklore about how the temple came to be established here says that a local Chieftain, Vakkay Kaimal, had a dream one night in which some mysterious person appeared before him and told him that four idols have been washed ashore and that these idols are to be consecrated at such and such places. The Kaimal being an ardent devotee hastened to the sea shore there lay four idols as indicated in the dream. They were duly installed in four temples as directed in the dream. Rama at Thriprayar (22 Km North west of Irinjalakuda) Bharata at Irinjalakuda, Lakshmana at Moozhikulam (30 KM south west of Irinjalakuda) and Satrugna at Payammal (5 KM south of Irinjalakuda). It is believed that worship at all these four temples on the same day is especially meritorious. Ardent devotees used to make it even in those far off days when they had to cover the entire distance by foot or in bullock carts. It has become very easy now a day. In the Malayalam month of Karkidakam (July 15th to August 15th) – the Ramayana Masa, thousands of devotees do this special pilgrimge, which is popularly known as Nalambalam Tthozhal – a pilgrimage to the four temples.
The lord at Koodalmanikyam is Chathurbahu Vishnu with Conch, Chakra, Gada and Japamaala. The general belief, however, is that the Lord is Bharatha the brother of Sree Rama. He anxiously and devotedly awaited the return of Rama from exile for fourteen years and then learnt from Hanuman that Rama has reached the outskirts of Ayodhya. He was much relieved and happy. Baratha in that mood is worshipped here. Naturally Hanuman is also present at Thidappilly [the holy kitchen] A distinctive feature of Koodalmanikyam temple is that there is only one single Prathista. Even Vigneswara, usually found in all temples dose not find place here. Usually when Thulasi leaves are offered to the diety, its seeds invariably sprouts in the premises. How this has not at any time happened in this temple is a mystery. One explanation is that Thulasi plant being sacred; it is worshipped wherever it is found. Probably it is to forbid even such an object of secondary worship in the temple precincts that Thulasi is not allowed to grow by some unforeseen power.
Irinjalakuda in former days is believed to have the confluence of two rivers, the place name suggesting such a conjecture. The Lord at the confluence is thus known as Sangameswara. Though the two rivers (Kurumali river and Chalakudy river) have changed course and Irinjalakuda is no longer on any river bank, Arattu – the holy dip of the idol at the close of the Annual Festival, is held alternatively in these two rivers suggesting a previous connection with these rivers. There is a folklore relating to the name Samgameswara.One saintly person belonging to Taliparambu was on a strange mission. His objective was to collect the chaithanya of idols of important temples in Kerala for being transferred to the idol of the temple in his village. This he did by entering the Sanctum Sanctorum of the temples he visited and transferring the Chaithanya on to the conch in his possession. When he did the same in Irinjalakuda he accidentally fell down and the conch was broken instantly transferring the divinity of all idols he had acquired on to the idol at Irinjlakuda. Thus the idol in which merged the divine Chaithanya of several idols came to be known as Sangameswara. The Namboodiri Brahmins associated with the temple still make all their Sevaas in the name of Siva, Vishnu and Devi at Sangamesa Sannidhi itself.