Pagsanjan (pronounced "pag-san-HAN") is on a river of the same name.
You can take a bus from the Buendia bus terminal in Manila to Santa Cruz. It takes about 2-3 hours, depending on traffic. The buses leave very frequently, and the bus fare was 140 pesos as of January 2009. A cab driver in Manila should be able to direct you to the correct bus terminal. The last bus returning from Santa Cruz to Manila leaves at 7pm.
Once you arrive in Santa Cruz, you can take a jeepney to Pagsanjan for 10 pesos per person (as of March 2008).
Take the jeepney to the tourism office -- they will direct you to the river and find you a boatman.
Alternatively, you can take a motorized tricycle direct from the bus terminal to the boating station for 20 pesos per person (as of January 2009), saving the walk from the tourism office to the falls. You can now buy tickets directly at the boat stations.
The trip up-river to the falls is the main attraction here. There is a standard fare for a boat ride, regulated by the tourism office. It is 1250 pesos per person including insurance (February 2013). Tipping is optional, but a small tip for each boatman (there are two per boat) is expected.
Alternatively, there is a second way of reaching the falls without having to take a boat (if you prefer hiking/adventure or if the water level does not permit the boats to access the falls). Access is done through a resort in Cavinti, Barangay El Pueblo. To reach the resort, go to Pagsanjan town, from where you can take a jeep to Cavinti (tell the driver you want to get to Barangay El Pueblo in Cavinti) for P15. From there, take a tricycle to the resort uphill for P50. The resort entrance is P270 per person and you are expected to tip the guides that help you throughout the trip. Part of the trip includes climbing down ladders, during which you will be secured with harnesses.
The newly opened BDO (Banco De Oro) has an ATM machine and accepts major cards. Traveler's checks might be accepted at the PNB, but expect a long wait and you'll need a photocopy of your main passport page.
Half-way through the boat ride, there is a stop where you can buy food on the river. Chicken, eggplant, rice, beer, buko juice, and drinks are for sale.