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Freshwater fish communities in Ecuador exhibit some of the highest levels of diversity and endemism in the Neotropics. Unfortunately, aquatic ecosystems in the country are under serious threat and conditions are deteriorating. In 2018–19, the government of Ecuador sponsored a series of workshops to examine the conservation status of Ecuador's freshwater fishes. Concerns were identified for 35 species, most of which are native to the Amazon region, and overfishing of Amazonian pimelodid catfishes emerged as a major issue. However, much of the information needed to make decisions across fish groups and regions was not available, hindering the process and highlighting the need for a review of the conservation threats to Ecuador's freshwater fishes. Here, we review how the physical alteration of rivers, deforestation, wetland and floodplain degradation, agricultural and urban water pollution, mining, oil extraction, dams, overfishing, introduced species and climate change are affecting freshwater fishes in Ecuador. Although many of these factors affect fishes throughout the Neotropics, the lack of data on Ecuadorian fish communities is staggering and highlights the urgent need for more research. We also make recommendations, including the need for proper enforcement of existing environmental laws, restoration of degraded aquatic ecosystems, establishment of a national monitoring system for freshwater ecosystems, investment in research to fill gaps in knowledge, and encouragement of public engagement in citizen science and conservation efforts. Freshwater fishes are an important component of the cultural and biological legacy of the Ecuadorian people. Conserving them for future generations is critical.