Enter the cave past Snake Eyes Shirahagi and look up to find a grapple spot. Climbed up, crouch to get past first low hanging stone and turn left to jump up the cliff, then follow the path to reach a pit of walls with footholds: execute a series of consecutive wall jumps to end up behind a giant statue and grapple on top to collect the Prayer Bead.
From the Water MillSculptor's Idol, going past the bridge after O'Rin and up to the house, there is an opening to the right-side of the house's stairs Wolf can crouch under: proceding beneath the build, Sekiro will encounter a Shinobi Floorboard. Going outside the house and grappling onto the second floor, the Prayer Bead can be found inside a shrine.
In the shrine with Long-arm Centipede Giraffe, there is a hole in the ground: drop down, crouched, keep the left until coming across a chasm. Looking up, there will be multiple grapple spots and keeping the right will lead to the Prayer Bead guarded by Lesser Centipedes.