The underground river is listed at one of the seven wonder of the world so it is still worthwhile to witness its splendor but the tourism board of Puerto Princesa should revamp all the system.
Depending on your location, it can be a long ride from PP. If you are in Sabang, well it is much faster.
However, once you secured your permit, the chaos starts! You have to board a small banca for a twenty minutes rides to the debarkation point. They are equipped with a 2 stroke engine without exhaust and can only accommodate 8 pax so better be ready to be deaf and squeezed by the time you arrive.
Then you go to the entrance of the cave where you wait for your turn to get into one of the few paddle boats.
You will have a boatmen/tourguide who will row and give you informations as you go, so do not expect them to pass on any scientific or accurate information. Stalagmites are named Virgin Mary and her candle, pineapple, or eggplant.... At the bow of the boat, one tourist will have to hold the light and try to follow instructions given in a broken english as to where to point the light.
You will only go 1.5km inside in the cave, you cannot go any further. When you ask why, they just tell you they do not have enough boats so they do a quick tour to accommodate the next batch as soon as possible.