AbstractThe world's large river systems are under increasing stress to support growing populations and economies. Balancing inevitable fluvial alteration with protections of river ecosystems will require awareness of lessons learned in big river systems where system‐scale alterations have already occurred. In 1985, the Interior Least Tern (Sternula antillarum; terns) was listed as endangered, citing “alteration of natural river dynamics” as cause for population declines. We refer to this as the “fluvial alteration hypothesis” and examine it by attempting to answer two primary questions: [Q1] What are the first‐order physical and hydrologic metrics associated with tern nesting reach selection at the regional scale? [Q2] Did human‐induced changes in these metrics differ between regions where tern breeding populations have recovered and where it has been stable or declined? We compiled metrics of sandbar nesting habitat across the nesting region for modern conditions and used regression modeling to assess the relative effects of each metric on nesting reach selection. At the scale of a nesting region, terns selected for nesting reaches that are wider have greater potential to braid, and are less likely to flood during nesting season. A comparison between subregions indicates that modern tern nesting conditions are substantially better in the lower Mississippi River and tributaries (LMRT) systems than the Missouri River and tributaries (MORT) system. However, both subregions had nearly equivalent sandbar nesting habitat quality prior to major human modifications. The fluvial alteration hypothesis was consistent with geomorphic assessments for the MORT system, but overlooked potential for human alterations to have differing, even beneficial effects to tern nesting habitat in the LMRT system.