Yamunotri, which is
north of Haridwar in the Himalayas Mountains, is where the holy Yamuna
River begins. It is about 234 km north of Haridwar. Technically the source
of the Yamuna is Saptarishi Kund, a glacial lake. To get there you have
to climb from Yamunotri 12 km right up the mountain., From Yamunotri the
Yamuna flows south until it reaches Delhi. It then flows to Braja Mandala
through Vrindavana and Mathura. From there it goes through Agra and eventually
merges with the Ganges and the underground Saraswati at Prayag (Allahabad).
The main reason it is so sacred is because it flows through Vrindavana and Mathura, and was thus intimately connected to Lord Krishna's pastimes.
The Yamuna River and the Ganges are considered the most sacred rivers in India.
"As far as sanctity is concerned, the River Yamuna is more directly connected with Lord Krishna than the Ganges. The Lord sanctified the River Yamuna from the beginning of His transcendental pastimes in the world. While His father Vasudeva was crossing the Yamuna with baby Lord Krishna for a safe place at Gokula on the other bank of the river from Mathura, the Lord fell down in the river, and by the dust of His lotus feet the river at once became sanctified." (Srimad Bhagavatam 1.19.6)
A bath in this river is said to be one hundred times more purifying than a bath in the Ganges. The reason being that even though the Ganges was once touched by the feet of Lord Vishnu, it was the Yamuna where Lord Krishna Himself played and swam with His cowherd boyfriends; He also sported in its waters with the beautiful gopi damsels of Vraja.
The traditional bathing place of most pilgrims is at Kesi ghata, where Lord Krishna bathed after killing the Kesi demon. The Yamuna has been flowing here at Kesi ghata since ancient times. One who takes bath in the river Yamuna is freed from all past sins and contamination of this material world. That person will also gradually become a pure devotee and achieve liberation by returning to the spiritual world to personally associate with Lord Sri Krishna, the Supreme Personality of Godhead.
"According to the Varaha Purana, as quoted by Srila Jiva Gosvami, there is no difference between the water of the Ganges and the Yamuna, but when the water of the Ganges is sanctified one hundred times, it is called the Yamuna. Similarly, it is said in the scriptures that one thousand names of Vishnu are equal to one name of Rama, and three names of Lord Rama are equal to one name of Krishan." (Srimad Bhagavatam 1.19.6 purport)
"Simply by bathing in the Yamuna, anyone can diminish the reactions of his sinful activities." (Krishna Book, Chap 38)
"By taking bath in the Yamuna River people are liberated and become Krishna conscious." (Caitanya Caritamrita Antya 4.98 purport)
"There are many devotees in Vrindavana who regularly bathe in the Yamuna, and this cleanses all the contamination of the material world." (Srimad Bhagavatam 5.8.31)
"One should not give up the process of austerity. If possible, one should bathe in the water of the Yamuna. This is an item of austerity. Therefore, our Krishna consciousness movement has established a center in Vrindavana so that one may bathe in the Yamuna, chant the Hare Krishna mantra and then become perfect and return back to Godhead." (Srimad Bhagavatam 6.5.28 purport)
"The Yamuna River washed Krishna's lotus feet when the Lord appeared in Vrindavana five thousand years ago. Lord Krishna sported daily with His boys and girlfriends in the Yamuna River and consequently that river is also caranamrita." (Srimad Bhagavatam 11.6.19)