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Abstract: Ecuador is one of the smallest and most densely populated countries in South America. In spite of this, it is also one of the 17 megadiverse countries worldwide and home to the largest number of species per unit area. Most aquatic ecosystems in mainland Ecuador have historically faced strong environmental pressures because the country’s economy has been based on the exploitation and trade of raw materials and agricultural products at a very high environmental cost. In this review, we provide a broad overview of the diversity of freshwater ecosystems and fish in mainland Ecuador. We address broadly current and historical threats to these ecosystems, including pollution due to oil extraction, mining activities, agriculture and the disruption of hydrological connectivity caused by hydroelectric dams. Despite these problems, we show some examples of promising initiatives at the local and national levels to address this situation.