The goal of this study was to address applied conservation ecology needs on the water basin scale within the Choco-Andes Conservation Corridor pilot area in northwestern Ecuador. The immediate conservation priority in this region was to describe baseline conditions of stream health prior to the development of a second crude-oil pipeline for the country. This study presents data on the density, biomass, diversity and trophic structure of benthic macroinvertebrates at riffle and bank habitat types from 4 rivers within the pilot region of the Choco-Andes Conservation Corridor. The objectives of the study are: (1) to understand local and regional influences on river health; (2) to document baseline data of 4 rivers prior to the development of a crude-oil pipeline; and (3) to provide assessment protocols and recommendations to the Maquipucuna Foundation.