ABSTRACT: Historical flow records are used to estimate the regulatory low flows that serve a key function in setting discharge permit limits through the National Pollutant Discharge Elimination System, which provides a nationwide mechanism for protecting water quality. Use of historical records creates an implicit connection between water quality protection and climate variability. The longer the record, the more likely the low flow estimate will be based on a broad set of climate conditions, and thus provides adequate water quality protection in the future. Unfortunately, a long record often is not available at a specific location. This analysis examines the connection between climate variability and the variability of biologically based and hydrologically based low flow estimates at 176 sites from the Hydro-Climatic Data Network, a collection of stream gages identified by the USGS as relatively free of anthropogenic influences. Results show that a record of 10 to 20 years is necessary for satisfactory estimates of regulatory low flows. Although it is possible to estimate a biologically based low flow from a record of less than 10 years, these estimates are highly uncertain and incorporate a bias that undermines water quality protection.