Four observations from two case studies are presented: physical habitat analysis of the Virgin River in southwestern Utah and upper Animas Basin in southwestern Colorado. The Virgin River is usually considered a sand bed river. Cross-sectional measurements, made at three streamflows, show there was considerable change in the channel between the times of the three sets of measurements. First observation: it is important to keep the three sets of data as individual data sets. Second observation: the channel index is not fixed in a river with a moveable-bed and changes affect understanding of the aquatic system. The Animas River has a wide range of streamflows and high metals toxicity. Both winter and spring discharges may limit trout populations. Third observation: (from Animas River) habitat time series analysis should be done with a model that specifically links physical habitat relations and streamflows. Fourth observation: annual time series of habitat suitability considering metals toxicity can be generated. Considering the third and fourth observation together leads to the secondary observation that the hydraulic and stream flow conditions that favor one species may not be as good for the species favored by the water quality conditions.
