Because Blue Agate is a huge category with Fire, Lace, Turkish, and other Agates, it’s associated with endless colors and tones.
The Crown, and Throat Chakras are mainly associated with Blue Chalcedony. Psychics and seers say it’s an awakening stone that brings enlightenment, intuition, and creativity. 
Blue Agate also opens the Root, Solar Plexus, and Heart Chakras when seen with multicolored Agate varieties. This crystal also links to the Stellar Gateway and Soul Star Chakras. They help you go beyond dimensions. 
Blue Chalcedony is linked to the elements Air and Wood and the planet Mercury. Air and Wood bring manifestation and stability, while Mercury pulls wisdom to you. 
Many cultures have sea and sky Gods or deities associated with Blue Agate. Some are Mithras, the Persian God of Light; Poseidon, the Greek God of the Sea; Amun, the Egyptian God of Creation; and Varuna, the Hindu God of the Ocean.
The Blue Agate properties also include freedom and peace, linked to the cosmic vibration number 5.