Nothing is secret actually, Truth is right here, right now.
But ancient wisdom has been coded in the way that it could remain available to the people even after thousands of years of it's revelation to great ancient mystics of the world.
They have coded in the things which are a) naturally found on earth, b) metaphorical stories and c) architect(temples and monuments)
Ever wondered what is so sacred about the meeting point of three rivers, like we have "Triveni Sangam" at Prayag? After all, it is just a natural occurrence and can be taken for granted. Why do we give so much respect to a river? Even if water of Ganges has a medicinal value, still what is so "holy" about the Ganges?
Same question goes for Kaaba? It is just a stone. Why is Nataraja a "LORD", if it is just an ordinary guy waving his arms and legs somewhere in the Himalayas?
No doubt rivers give vegetation to the region they pass through, and we must show our "gratitude" towards these rivers which make life possible in different forms. Yet there is nothing "holy" about them.
We have two subtle channels or "naadis" which are coiled together like serpents around our spine and they carry life force energy ((like rivers carry life force energy for vegetation)) called "Prana" in Sanskrit and "Chi" in Chinese traditions. There is another naadi called Shushumna which runs through the center of the spine and remains invisible until it meets the meeting points of ida and pingala which is located between our eyebrows. All yogic kriyas or breathing exrcises including pranayam are meant to activate the "Shushumna" naadi which awakens the "Third Eye" of wisdom and Yogi becomes one with the supreme and attains Moksha.
Ganga and Yamuna are representation Ida and Pingala and Saraswati which is an "invisible(mythical) river is said to meet at Prayaag with Ganga and Yamuna and this adds sacredness to this point and the place becomes of great religious value.
The same is true for a city called "Varanasi" which literally means "Beyond Nostrils", vara means beyond and nasi means nostrils. So it again correspond to the same point called "Third Eye" in human body.