By ship
Guayaquil´s port is the biggest in Ecuador. You can travel to Galápagos Islands and other destinations from here.
By plane
The new José JoaquÃn de Olmedo International Airport [ (http://www.tagsa.aero)], elected as best South American Airport, is located near the new business district center and is next to the International bus station. In this airport, you can find daily flights to New York, Miami, Houston, Buenos Aires, Caracas, Madrid, Amsterdam, Lima, Bogotá, Panama City, San José, San Salvador, etc; and a new 4 times a week to Cali and twice a week to MedellÃn Colombia. Taxis to a hotel in the northern suburbs shouldn't cost more than $3 and a ride to downtown, where most attractions are located, is about $5. Currently there are plans to build a new international airport for about 20 minutes from Guayaquil, near Daular.
If you are planning to visit the Galapagos Islands, Guayaquil is the cheapest place to take a flight from. There are three air carriers that will take you across the Galapagos Islands as well as the Ecuadorean mainland, LAN-ECUADOR (http://www.lan.com), Aerogal (http://www.aerogal.com.ec) and TAME (http://www.tame.com.ec) have non stop daily flights, departing from Guayaquil is cheaper than leaving from Quito(Is closer and most of the Quito flights do make an stop at Guayaquil's airport for Refueling and picking up passengers.
International departure airport tax was just recently increased in Guayaquil and is exactly $29.75 January 2010. About 15$ cheaper than Quito airport.
By bus
Cruz del Sur operate international bus services to and from Peru.
Within the city the local bus system is confusing but the locals will help you get where you want to go. It is also the cheapest way to get around the city as there is no metro system. For women it is safest if you sit at the front near the driver but don't be alarmed the bus is a safe way to travel around Guayaquil.
Guayaquil's bus terminal is well organized, but still keep an close eye on your belongings. There are frequent connections to almost every destination in Ecuador. Keep you items close to you during the midnight check points. The police will steal valuables when the men leave the bus to be checked for weapons, this occurs on night busses around Ecuador.
By car
If you are driving, your horn is your best friend. Be careful, as the city is full of aggressive drivers, but if you are always on the defensive you won't get anywhere. Gas stations are full service.
You can also rent a car cheaply just outside the airport, paying around $35 a day, Carmax is one of the less expensive yet reliable companies available.