One of the biggest challenges when conducting a national-scale assessment of lakes, such as the 2007 US National Lake Assessment (NLA), is finding enough reference lakes to set appropriate expectations for the assessed sites. In the NLA, a random design was used to select lakes for sampling to make unbiased estimates of regional condition. However, such an approach was unlikely to yield enough minimally impacted lakes to use as reference sites, especially in disturbed regions. We developed a 3-stage process to select candidate reference lakes to augment the NLA probability sample in the northeastern USA (Northeast). Screening included a water-chemistry database filter, landuse evaluation, and analysis of aerial photographs. In the Northeast, we assembled a database of 2109 lakes >4 ha in surface area, of which 369 passed the water-chemistry screen. Of these, 220 failed the watershed landuse screen and 60 failed the aerial photograph screen, leaving a set of 89 optimal candidate reference lakes. Twenty of these lakes were sampled as potential reference lakes in the NLA. Based on a wide variety of indicators, NLA field measurements indicated that almost all (85–100%) of the chosen candidate reference lakes had least-disturbed water chemistry, although somewhat fewer had least disturbed physical habitat (74–79%) and biology (68–78%). Nevertheless, our 3-stage screening process was an efficient method for identification of good candidates for reference-lake sampling. The reference-lake selection process used in our study can be done in the office and relatively inexpensively. As such, it is very useful for large-scale regional or national studies encompassing areas too large to census. It also has the advantage of adding a level of consistency and quantification to the reference-site selection process.