The nested clade analysis can be extremely useful in testing for an association between genetic variation and geography and in explaining these observed patterns in terms of historical or contemporary population processes. The strength of this method lies in its ability to test a variety of processes simultaneously under a rigorous statistical framework. Indeed, many recent studies have used the nested analysis in a wide range of terrestrial and aquatic taxa. However, it has been suggested that riverine, riparian, or coastal species may be better examined using river (or coastal) distances rather than the standard geographic (great circle) distances among populations. It is thought that the standard geographic distances may not adequately describe the actual distances involved between populations of species inhabiting these one-dimensional (riverine) habitats. Therefore, we analyzed population data from an Ozark crayfish, Orconectes lutetus, to examine the effects on the results of a nested clade analysis using river distances. In most cases, the haplotypes detected in this crayfish were unique to a particular drainage or a group of neighboring drainages, indicating very little movement of individuals among drainages. Five major population groups were detected, corresponding to many of the major river drainages sampled in this study. The two types of distance analyses obtain similar results for higher-level (older) clades, but differ in many of the inferences made for lower-level (younger) clades. However, we suggest that the comparison of both types of analyses for riverine species may enhance the process of elucidating historical and contemporary population processes, especially in cases where the transfer of individuals among different drainages are involved.