Commercial raft trips and guide services should include transportation from their office location or meeting place for the trip to the river, and back. For trips that don't base in Quito, this usually means that you must travel to the local meeting place in Tena, Baņos, Macas, etc, on your own, unless it is specifically included in the cost of the trip.
Paddlers will find that Ecuador is one of the easiest places in the world to travel with a kayak. Some groups may prefer to hire a van or a truck with a driver for their entire trip, but most people use public buses to move long distances between cities, and hire taxis locally to get to and from the river.
Almost all of the buses have spacious under storage areas. It is NOT customary to pay more for the kayak, unless the bus stops en route and has to wait while loading, in which case $1 per boat should be sufficient. As a simple precaution, try to have all of your gear packed securely in your kayak, or inside of gear bags to discourage theft. Keep all valuables either within sight and on your lap or stored in the secure under storage compartments while on buses, and be alert.
In most of the paddling towns, the local "taxis" are double-cab pickup
trucks, which charge very reasonable fares. In Quito, Santo Domingo de
los Colorados, and Baņos, you may have to get more creative and seek out
the owner of a suitable shuttle vehicle. Always confirm the price of the
shuttle or taxi before the trip, and make sure to have tie-down ropes
or straps handy, and that all boats, paddles and equipment are secure.
Only leave dry clothes and personal items with known and recommended drivers.
Bus Schedules: Quito - Baeza - Tena This is the most direct route to Tena. Also serves the Quijos River Valley.
Bus Schedules: Tena - Baeza - Quito Return schedules.
River Beta Guide to Rafting & Kayaking in Ecuador