Quito & Highlands: Quito is broadly representative of the Highlands region as a whole and September stays bright, dry and sunny.
Oriente/Amazon: By comparison to earlier, far-wetter months of the year in the Oriente, this month is a dry one. Rainfall is generally down: in Parque Nacional Yasuni monthly precipitation is not much off its annual low. Jungle roads and paths are about as good as they get: free of landslides (well, mostly!) and firmer underfoot.
Desert Coastal Strip & Galapagos: Almost no rain whatsoever falls along the coast this month: Guayaquil, broadly representative of coastal Ecuador, records an average rainfall of just 0.03 inches/ 1mm. There are comparatively cool temperatures (not to mention fog) all along the seaboard.
Fog and cooler, drier weather also continues in the Galapagos (the coolest, driest weather of the year in fact), with nutrients reducing water clarity (but making it more appealing to dive or snorkel in because more sea creatures are attracted by nutrients).
Crowds & Costs
Whilst weather remains favorable for a visit to the Highlands or the jungle (if you like exploring the jungle from the land, especially), visitor numbers are way down. September, along with October and November, is a good month to try and negotiate deals on accommodation, tours, and other services. You may also get good deals on the coast this month, where low season continues, and even on the Galapagos, where cooler flatter weather reduces visitor numbers.
Where to Go
Quito & Highlands: September is still prime outdoor activity weather in the Highlands of Ecuador. In Quito, spend time climbing to some of the many viewpoints, or take the TelefériQo up to volcanic peak Volcán Pichincha. Head south to Latacunga to hike the Quillota Loop or have an adventure in Parque Nacional Cotopaxi, full of volcanoes and memorable trails.
Near Cotopaxi, stop off in Latacunga for that city's big annual festival. Near Cuenca, the best place to hike this month now that some of the driest weather of the year has reached it is Parque Nacional Cajas, high lake-spattered moorland and mountain full of dwarf forests of polylepis trees, some of the highest forests in the world. 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 is a good place to visit this month, where jungle hiking trails are quite dry and where elaborate canopy walkways make it possible to see birds sunning themselves in the canopy in the increased sunshine. Another good place to base yourself might be Puyo, a place from which to visit the central jungle. Agencies here offer land-based jungle trips to spots within a few hours' journey from town.
Desert Coastal Strip & Galapagos: Probably the place to base yourself on the coast in September is Puerto López. It has hiking in nearby rainforest and trips to the Isla de la Plata, where you can observe whales and other marine animals and birds. Guayaquil is a vibrant and interesting city, with a rejuvenated waterfront, several diverting museums and fantastic nightlife, so the cool, overcast September weather will not worry you too much. Or head to Machala for their festivities celebrating the banana, the main local crop.
What to Do
Quito & Highlands: In August, walking is the key activity in the Highlands. Even Quito has many beautiful viewpoints that you can walk to or take a gondola-cable car. Quito's TelefériQo transports you up the slopes of Volcán Pichincha, a volcano, to nearly 13123 feet/4,000m. There are superb treks to do in the mountains, such as the Quillota Loop or hikes in Parque Nacional Cotopaxi, which is full of spectacular volcanoes. Neither are far from Quito.
Another good place for diverse outdoor activities is Banos, where you can try mountain-biking on the Ruta de las Cascadas (Waterfalls Route) to Puyo, bungee-jumping or bathing in natural thermal pools.
Oriente/Amazon: 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: that which lives on or in the trees, such as snakes and spiders!
Desert Coastal Strip & Galapagos: Coastal fog keeps lingering along with that cooler weather, so many find it a good time to try some coastal hiking, as it is colder for sitting around on the beach. Puerto López, north of Guayaquil, remains a great coastal base in September. 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.
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. However, increased nutrients in the waters increase sightings of blockbuster marine animals, such as the whale sharks, as well as other nutrient-loving sea creatures. Penguins, sea lions, blue-footed boobies, and albatross are some of the animals and birds active on the islands this month.
Fiesta del Yamor: First week of September. This happens in that city of many festivals, Otavalo, and celebrates the drink called yamor, made from seven sorts of corn, with lots of singing, dancing, and merry-making.
Feria del Banano: Third week of September. Happening in southern city Machala, this festival celebrates the banana, the main food crop hereabouts.
Fiesta de Mamá Negra: 23/24 September. This is one of the most famous and biggest festivals in the Highlands, taking place in Latacunga. This is a grand display of pageantry and merry-making, where performers dress up as indigenous Amazonians, enslaved African people and conquistadors (all caricatured equally) to represent the different components in the founding of Ecuador.