Augments can be upgraded by using higher quality level augment resonators. Combine similar augment resonators with special toolkits sold by Minister of Ca’ d’Oro NPCs in Venice to create higher quality level augment resonators. For example, combine two "Attuned Mending Augment Resonator (level 1)" with one "Augment Amplifier Kit (Level 2)" to create an "Attuned Mending Augment Resonator (level 2)."

Rare (blue), epic (purple), and legendary (gold) augments resonators can be upgraded to higher quality levels just like uncommon (green) augment resonators.

For rare, epic, and legendary augments, you may first have to acquire "unattuned” augment resonators by completing Elite and Nightmare Scenarios and "attune” them by combining them with Augment Attuning Kits before you can use them to unlock those augments. The tooltip for an unattuned augment resonator will tell you what is required to attune it.