Improved flood-frequency estimates for short-term (10 or fewer years of record) streamflow-gaging stations were needed to support instream flow studies by the U.S. Forest Service, which are focused on quantifying water rights necessary to maintain or restore productive fish habitat. Because peak-flow data for short-term gaging stations can be biased by having been collected during an unusually wet, dry, or otherwise unrepresentative period of record, the data may not represent the full range of potential floods at a site. To test whether peak-flow estimates for short-term gaging stations could be improved, the two-station comparison method was used to adjust the logarithmic mean and logarithmic standard deviation of peak flows for seven short-term gaging stations in the Salmon and Clearwater River Basins, central Idaho. Correlation coefficients determined from regression of peak flows for paired short-term and long-term (more than 10 years of record) gaging stations over a concurrent period of record indicated that the mean and standard deviation of peak flows for all short-term gaging stations would be improved. Flood-frequency estimates for seven short-term gaging stations were determined using the adjusted mean and standard deviation. The original (unadjusted) flood-frequency estimates for three of the seven short-term gaging stations differed from the adjusted estimates by less than 10 percent, probably because the data were collected during periods representing the full range of peak flows. Unadjusted flood-frequency estimates for four short-term gaging stations differed from the adjusted estimates by more than 10 percent; unadjusted estimates for Little Slate Creek and Salmon River near Obsidian differed from adjusted estimates by nearly 30 percent. These large differences probably are attributable to unrepresentative periods of peak-flow data collection.