In recent years, pollution of watercourses in nearby protected ecosystems has increased due to urbanization. Standard physiochemical methods and probes are one way to monitor watercourses for quality. However, they often do not provide the full ecological status of the body of water. In this work, we set out to assess the ecological water quality of an urban stream by using benthic macroinvertebrates as bioindicators. We conducted the work on the Orienco stream in Lago Agrio in the province of Sucumbíos in the Northern Ecuadorian Amazon (NEA). The stream has become a sink of raw domestic sanitary wastewater from rural and urban areas. A total of 4511 macroinvertebrates from 10 families were identified across 17 sampling points. We compared our results from the biotic indices derived from the macroinvertebrates to standard water‐quality parameters (temperature, conductivity, dissolved oxygen, biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia–nitrogen, and pH) simultaneously sampled in the stream. The standard parameter results indicated that the water‐quality levels of the stream met the Ecuadorian water‐quality criteria most of the time. However, the results from the biotic indices classified the stream water as poor or very poor water quality. The results from the Biological Monitoring Working Party, Average Score per Taxon, and Family Biotic Indices had overall scores of heavily polluted waters of 45, 4.5, and 8.74, respectively. Furthermore, these results were consistent with reduced richness and evenness, and overall lower Shannon diversity and relatively higher Simpson Dominance indices of 0.71 and 2.56, respectively. We conclude that the macroinvertebrates were better indicators of the ecological water quality of the Orienco stream than the water‐quality parameters from standard methods and probes alone. Our findings highlight the need for more integrated ecological assessments, which can provide critical information to the management and conservation strategies of urban watercourses in the NEA region. Integr Environ Assess Manag 2023;19:615–625. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).