At the end of Chapter 13, Ryu must swim through the aquaducts (again) to reach the platform leading to a battle with Lord Doku.
You can use this section to farm some yellow orbs. Save here and equip the Spear Gun. Before riding the platform to the battle (or even just after, at the start of Chapter 14), swim back under the passageway and into the lift room (the one full of Shark Creatures).
Each monster is worth 1000, so you can collect about 6000 each time you go through the place. Swim just to the bottom of the tunnel and then back, allowing the creatures to respawn, then repeat. Do this for a few minutes, and then be sure to visit the conveniently placed Muramasa's shop statue to fully power up all your weapons and stock your inventory.