Ecuador is divided into three distinctive climatic zones (four, if you count the coast and Galápagos as separate).
Quito & Highlands: Quito is broadly representative of the climate in the Highlands region. Weather is cooler in the Quito area right now, with rain as much in evidence as sun. At this time of year, daily highs in Quito are around 68.7°F (20.4°C).
Oriente/Amazon: Ecuador's Amazon climate varies because this is a vast region. Overall, this is the second warmest month of the year in Parque Nacional Yasuni, and with rainfall down to just 7.63 inches/194mm, the driest month overall since February.
Desert Coastal Strip & Galapagos: It's still muggy on Ecuador's coastline, although this is clearing up and becoming more pleasant, with bluer skies towards the end of this month. After several months of bone-dry weather, rain is slowly starting to increase in evidence. Average temperatures increase for a fourth straight month, in preparation for the start of better beach-going come December.
This is an unsettled month in the Galápagos, with change in the air: the water stays cool with increasing showers as the climate gears up for entering the warmer, wetter season which is on the horizon.
Crowds & Costs
November is a quiet month in the Highlands, a busy one in the Oriente, whilst on the coast and in the Galapagos it is hardly busy, but gradually getting busier. November, along with September and October, is a good time to look for deals in the Highlands, on the coast, and in the Galapagos. Thanksgiving in the US sees a spike of visitors to the Galapagos in the latter part of the month.
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Where to Go
Quito & Highlands: Ecuador has superb cultural heritage: Quito and Cuenca were two of the world's first cultural destinations to be listed by Unesco. So Quito, and particularly Cuenca, are great to explore right now. Cuenca is at its best at the beginning of the month for the three-day party culminating in its independence day.
Cuenca's surrounds also lend themselves well to exploration. The handicrafts villages and towns in the green nearby valleys, like Sigsig, have superb hiking (especially at the community of Principal) as well as great artisan shops to check out, so there is something to do come rain or shine!
Parque Nacional Cajas near Cuenca is also in one of its driest periods. This high lake-spattered moorland and mountain is also carpeted in tracts of dwarf forests of polylepis trees, some of the highest forests in the world. Finally Baños, on the cusp between mountains and jungle, also has lots of outdoor activities on offer: see below for more details.
Oriente/Amazon: Parque Nacional Yasuni remains a good place to visit this month, and is, as in other months, a favorite destination with foreign travelers. Here, jungle hiking trails are quite dry and some lead to elaborate canopy walkways where it is possible to see birds sunning themselves in the canopy in the warm and sunny spells of weather.
Desert Coastal Strip & Galapagos: Weather might be improving on the coast, and you may, if you are accustomed to cold northern hemisphere weather, be happy trying out beaches such as those at Mompiche, Canoa or Montañita.
Or consider basing yourself at Puerto López, north of Guayaquil. It has hiking in nearby rainforest and trips to the Isla de la Plata, where you can observe marine animals and birds such as blue-footed boobies in an ecosystem very similar to that of the Galapagos and with much of the same flora and fauna (but at a much-reduced cost!). Water is cooler in November on the Galapagos, so it's worth considering round-island wildlife cruises which you might be able to snap up at a bargain price at the moment.
What to Do
Quito & Highlands: Try exploring colonial architecture and museums in Quito or Cuenca, shopping for handicrafts in Otavalo or the Cuenca valley handicrafts towns and villages, all of which have great hiking if the weather is favorable.
Or if you are in Cuenca, attend the festivals at the beginning of the month! Baños is a brilliant destination with an abundance of activities that don't necessarily depend on the sun or the rain: good at this unsettled time of year. As at Papallacta further north, there are great natural thermal baths to soak in (if it's cold), hikes and bike rides (if it's sunny) and bungee-jumping whatever the weather as long as it is not too wild or windy.
The Ruta de las Cascadas (Waterfalls Route) between Baños and Puyo might just be starting to be truly spectacular again if rain has swelled the waterfalls.
Oriente/Amazon: With water levels far lower than average, this is the perfect time to explore the jungle on its pathways. Some of these lead to canopy walkways that are great for watching the forest from above (in the drier sunnier weather birds love sunning themselves on the canopy). You also see different wildlife to that on the rivers: that which lives on or in the trees, such as snakes and spiders, plus some interesting plants.
Some lodges run ethnobotanical tours at this time of year which explain insect and plant medicinal uses, and how tribes have utilized the rainforest's rich variety of plant life for food, healing and practical things like bow and arrow making for centuries.
Desert Coastal Strip & Galapagos: If you are accustomed to northern hemisphere winters, you might want to try beach-going on Ecuador's lovely beaches, although the coastal fog keeps lingering and it's not that warm. If it's too cold to swim, you could walk along the beach or go hiking near Puerto López, north of Guayaquil. Here you are well placed for trekking in the teeming rainforest of Parque Nacional Machalilla, with excellent hikes and beaches and an indigenous community at Agua Blanca.
Then, of course, there are the boat trips to Isla de la Plata, where much of the same wildlife visible in the Galapagos can be seen. This is also a brilliant month for diving and snorkeling in the Galapagos. Water visibility is less than the first half of the year, but still decent.
What makes water-based activities amazing, though, is the increased nutrients in the waters which attract blockbuster marine animals, such as the whale sharks, as well as other nutrient-loving sea creatures. Other animals and birds active on the islands this month include the fur sea lions, which spend a lot of time on beaches around now, blue-footed boobies and frigate birds, famous for their elaborate mating ritual which involves puffing up their red chests.
Cuenca Independence Day: November 1-3. Cuenca's independence day is the day after the two nationally important holidays of All Saints' Day and All Souls' Day, making this southern Highlands city the place to spend this mini-vacation because it turns into a long weekend of partying, with live music performances, dancing, singing and other cultural events.