The map is procedurally generated. Map layout, Number of Secrets and Secrets Locations will vary for each playthrough. One Secret Rune can be collected only after you have completed the entire main campaign. So, in your first playthrough you wont be able to collect all the secrets. Check the video at the end of the page if the written walkthrough is not clear.
This secret is inside a crypt. Near to the crypt entrance there is an area hard to access. You need to be in a correct position to be able to jump across revealing the secret chest.
From the first secret, turn around and jump across. then get down the narrow stairs. At the bottom a secret door will be revealed. Enter it to collect a secret chest. This secret might be impossible to get if you dont get the correct camera angle in the playthrough.
Secret 3 (Can be collected only after completion of Main Campaign)
This secret is in the area where you get the objective to find the golden key. Next to the room with the golden key, you’ll find a switch behind a tree. Interact with the switch to open a secret passage. Go inside and collect a Secret Rune. Collecting 9 Runes will unlock a Secret Cow Mission.