Like other Andean Amazon catchments, the Pastaza River Basin is a hotspot for biological, cultural, and geographical diversity, and one of the most rapidly changing areas on earth. Native communities have inhabited this landscape for hundreds of years, however modern industrial development (petroleum, leather, cement, textiles, hydropower) and expanding human populations exert increasing pressure on the landscape, especially freshwater resources.  For example, human sewage and industrial waste streams typically flow untreated into rivers; one large dam has already altered the natural flow regime of the Pastaza River and more hydropower projects are in planning stages.  The framework of integrated water resources management (IWRM) provides a space to address the intertwined issues that affect the quality and quantity of freshwater resources and the well-being of residents in the Pastaza River Basin.  IWRM is an applied process for meeting human water needs in an equitable and efficient manner without causing unacceptable degradation of freshwater ecosystems.  Here, we present results from a diagnostic study of the status of water resources in the Pastaza River Basin and discuss initial lessons learned from an on-going initiative to promote IWRM.  Analysis of biological and physicochemical parameters indicated that streams draining densely-populated areas were in fair or poor condition, and had higher concentrations of heavy metals, organic and inorganic nutrients, total suspended solids, and total dissolved solids.  Data from this study are now being used by water managers to encourage long-term collection of scientific data on water quality and facilitate collaborations between stakeholders in the basin.