The map is procedurally generated. Map layout, Number of Secrets and Secrets Locations will vary for each playthrough. In the first playthorugh there is only 1 Secret to be collected. One Secret Rune can be collected only after you have completed the entire main campaign. Check the video at the end of the page if the written walkthrough is not clear.
This secret is in the area where you have to power 5 beacons. You will have to jump across to a floting island to reveal the secret chest.
Secret 2 (Can be collected only after completion of Main Campaign)
This is in the area where you get the objective to find the Golden key. In this area you will have a room with blue key. left to the gate of this room you’ll find a pressure plate behind a tree. Press the plate to reveal a secret door in the room with blue key. Go inside and collect a Secret Rune. Collecting 9 Runes will unlock a Secret Cow Mission.