The whales need warmer waters than their northern habitat provides, shelter from predatorial orcas, and the increased bouyancy of the salty lagoon waters.
Whilst it is possible to view passing whales in places such as Ensenada, Todos Santos, Los Cabos and La Paz, the real close encounters take place in the three sanctuaries which form the calving areas on the Pacific coast.
The furthest north is nearly 450 miles from the US border at Guerrero Negro, just south of the 28th parallel which bisects the peninsula and forms the state line between Baja California (Norte) and Baja California Sur. Laguna Ojo de Liebre (Eye of the Jackrabbit Lagoon) is certainly a more poetic name than its name in English - Scammon's Lagoon, so named after a whaler who turned the waters red in the 19th century in his pursuit of whale oil.
Fortunately the whaling industry failed to completely eliminate the species, which has been protected since the 1940s, and now thrives in what was formerly a place of slaughter. As in the other two locations, only registered operators can launch their boats (pangas) into the lagoon. Ojo de Liebre is also home to dolphins and sea lions, as well as a bird sanctuary and the world's largest salt plant, which despite its size remains largely unobtrusive.
100 miles (160km) further south lies Laguna San Ignacio, a site free from any industrial presence (despite past threats). The lagoon is about 40 miles (65km) from the town of San Ignacio, along a graded dirt road, so you need to set off early to see the whales in the morning, which is the best time of day to see them. The alternative is to camp at the lagoon. San Ignacio itself is a pretty oasis town with an 18th century Spanish mission, which is well worth a visit if you're passing through.
Furthest south of the three breeding grounds, and therefore closest to the resorts of Loreto, La Paz and Los Cabos, is Bahia Magdalena. The lagoon here is situated near the deep-water port of San Carlos, and further north the smaller, more intimate Puerto Adolfo Lopez Mateos. Despite its relative proximity Bahia Magdalena is several hours from the resorts mentioned, so expect a long (and sometimes very expensive) day trip if you decide to do it that way.
High season runs from January to March, though it is possible to see them a few weeks either side (Mid December to Mid April). This is about wild animals in their natural environment, remember, and so nature takes precedence. This is not a purpose built tourist attraction!
Amongst the best operators (who have active websites at the time of writing), in Guerrero Negro I recommend malarrimo.com, who also have an excellent hotel/restaurant/RV park, and mariostours.com. In San Ignacio there's kuyima.com, and in Magdalena there's magbaytours.com. If you're staying in a resort there'll be local operators offering tours, but remember about time and distance (and cost!).
For me the ideal way to enjoy whale watching in Baja California is to build it into a tour of the entire peninsula. If you intend to drive the peninsula yourself then I say "Fantastic - You'll have a wonderful time!" If driving's not for you have a look at the rest of our site - we offer unique transpeninsular tours which include unforgettable whale watching excursions.Click for itineraries, dates and prices.