We present a system to derive benchmarks for protection of aquatic organisms that, as chemical criteria, promotes regulation of contaminants and, as biological criteria, focuses on an endpoint that adequately represents species abundance. The proposed method utilizes quantile regression to quantify the decline in maximum number of organisms with increasing contaminant concentrations. This limiting function then is applied to project the contaminant concentration associated with a threshold number of organisms. The threshold value is defined according to the study's objective and level of desired protection. Here, we defined it as 0.8 × 90th quantile of the number of organisms in samples from reference sites. We use the proposed system to derive taxonspecific, field-based effect concentrations (FECs) for copper and zinc in Ohio, USA, rivers and streams. Comparisons of results with respective chronic values suggest that only the draft criteria for copper are adequately protective. Projected zinc FECs were far lower than respective estimates of chronic values. The FECs likely are less sensitive to impacts of confounding factors because high numbers of organism in samples are observed when negative effects of other stressors are absent or minimal. We discuss other advantages, limitations, and potential applications of the proposed system.