Five of the nine populations of white sturgeon Acipenser transmontanus, located between dams on the Middle Snake River, have declined from historical levels and are now at risk of extinction. One step towards more effectively protecting and managing these nine populations is ranking factors that influence recruitment in each of these river segments. We developed a model to suggest which of seven mechanistic factors contribute most to lost recruitment in each river segment: (1) temperature-related mortality during incubation, (2) flow-related mortality during incubation, (3) downstream export of larvae, (4) limitation of juvenile and adult habitat, (5) mortality of all ages during summer episodes of poor water quality in reservoirs, (6) entrainment mortality of juveniles and adults, and (7) angling mortality. We simulated recruitment with, and without, each of the seven factors, over a typical series of hydrologic years. We found a hierarchical pattern of limitation. In the first tier, river segments with severe water quality problems grouped together. Poor water quality during summer had a strong negative effect on recruitment in the river segments between Swan Falls Dam and Hell's Canyon Dam. In the second tier, river segments with better water quality divided into short river segments and longer river segments. Populations in short river segments were limited by larval export. Populations in longer river segments tended to be less strongly limited by any one factor. We also found that downstream effects could be important, suggesting that linked populations cannot be viewed in isolation. In two cases, the effects of a factor on an upstream population had a significant influence on its downstream neighbors. ?? 2002 by the American Fisheries Society.