Taxis are plentiful and relatively inexpensive. Most trips from downtown to the northern Hotel Zone and Marina Vallarta cost 65 to 80 pesos; to or from Marina Vallarta to Mismaloya Beach (to the south) costs 195 pesos. Rates are charged by zone and are generally posted in hotel lobbies. Taxis can also be hired by the hour or day for longer trips. Rates run about 200 pesos per hour, with full-day discounts available -- consider this an alternative to renting a car.
Rental cars are readily available at the airport, through travel agencies, and through the most popular U.S. car-rental services, but unless you're planning a distant side trip, don't bother. Car rentals are relatively expensive, especially because of insurance rates, and parking around town can be very challenging, unless you opt for one of the two new parking garages constructed on either end of the malecón zone (at Park Hidalgo to the north, and adjacent to the northern border of the Cuale River to the south). If you see a sign for a cheap car or jeep rental, be aware that these are lures to get folks to attend timeshare presentations. Unless you are interested in a timeshare, stopping to inquire will be a (possibly annoying) waste of your time.
City buses, easy to navigate and inexpensive, will serve just about all your transportation needs. They run from the airport through the Hotel Zone along Morelos Street (1 block inland from the malecón), across the Río Cuale, and inland on Vallarta, looping back through the downtown hotel and restaurant districts on Insurgentes and several other downtown streets. To get to the northern hotel strip from old Puerto Vallarta, take the ZONA HOTELES, IXTAPA, or LAS JUNTAS bus. These buses may also post the names of hotels they pass, such as Krystal, Sheraton, and others. Buses marked MARINA VALLARTA travel inside this area, stopping at the major hotels there.
Other buses operate every 10 to 15 minutes south to either Mismaloya Beach or Boca de Tomatlán (a sign in the front window indicates the destination) from Constitución and Basilio Badillo, a few blocks south of the river. Buses run generally from 6am to 11pm, and it's rare to wait more than a few minutes for one. The fare is about 7 pesos. You do not have to have exact change; the driver will make change.
The muelle (cruise-ship pier), also called Terminal Marítima, is where excursion boats to Yelapa, Las Animas, Quimixto, and the Marietas Islands depart. It's north of town near the airport, an inexpensive taxi or bus ride from town. Just take any bus marked IXTAPA, LAS JUNTAS, PITILLAL, or AURORA and tell the driver to let you off at the Terminal Marítima. Note: Oddly enough, you must pay a nominal federal tax to gain access to the pier -- and your departing excursion boat.
Water taxis to Yelapa, Las Animas, and Quimixto leave multiple times per day starting at 10am and continuing until 6pm from the pier at Los Muertos Beach (south of downtown), on Rodolfo Rodríguez next to the Hotel Marsol. A round-trip ticket to Yelapa (the farthest point, which takes about 45 min. each way) costs 250 pesos. The latest return time is usually 4:45pm, but confirm the pickup time with your water taxi captain. Other water taxis to Yelapa depart from Boca de Tomatlán, about 30 minutes south of town by public bus. These can be a better option if you want more flexible departure and return times from the southern beaches. Generally, they leave on the hour for the southern shore destinations, or more frequently if there is traffic. Prices run about $15 round-trip, with rates clearly posted on a sign on the beach. A private water taxi costs about $35 per hour with a 4-hour minimum, allowing you to come and go on your own time. They'll take up to eight people for that price, so often people band together at the beach to hire one. There's also water taxi service from Los Muertos Beach to Paradise Village in Nuevo Vallarta for $12 each way.