Navojoa has two types of climates: semi-dry and semi-humid. Both are extremists with an average maximum temperature of 32.7°C (90°F aprox.) in June and July, and an average minimum temperature of 18.5°C (65°F aprox.) in December and January. The annual average temperature is 25.4°C. The rainy season presents in summer in July and August. Cyclones may present occasionally between September and October depending on the meteorological conditions.

Benefiting from the closeness of the mountains with the shore, the region has a milder climate and different types of vegetation.