Runes are obtained exclusively from the Cave of Runes, a special instanced zone you can enter from the cave system hub. The other cave, Cave of Crystals, drops gems for weapon levelling instead.
You need Cave Tickets to enter the Cave of Runes. Tickets are earned from active codes, daily quests, and community milestones. Each ticket grants one run in the cave.
Inside the Cave of Runes, you fight through waves of enemies and a final mini-boss. The deeper you go in a single run, the better the rune reward at the end. Clearing all waves guarantees a rare or higher-tier rune drop.
Save your Cave Tickets for longer sessions. A single focused session with multiple Cave of Runes runs is more efficient than one-off entries spread across different days.
Higher-difficulty dungeon runs also have a small chance to drop common-tier runes from boss kills, but the Cave of Runes is by far the most reliable source.