As societies increasingly use more water and other natural resources, the ability of managers to conserve aquatic biota will depend on whether habitat can be maintained or restored. However, managers must be able to track the status and trend of these aquatic systems if they are to be accountable to the goal of maintaining habitat conditions. This can be particularly challenging given that natural landscape and geomorphic characteristics can also have a strongly influence on expected stream conditions. Within the Interior Columbia River Basin and over the last decade, the PACFISH INFISH Biological Opinion Effectiveness Monitoring Program (PIBO EMP) is trying to answer the question; “Are key biological and physical components of aquatic and riparian communities being improved, degraded, or restored within the range of anadromous salmonids (Oncorhynchus sp.) and bull trout (Salvelinus confluentus)?” This program has sampled over 1300 stream reaches spatially distributed within the Basin. We assess status and trend by incorporating techniques that account for variation due to natural landscape and geomorphic characters. We have found that stream habitat conditions have been improving over the last 15 years but that the status of stream conditions vary greatly across the study area. Low-transport stream reaches in dry climates and stream reaches close to roads have been among the slowest to respond to management. Results indicate that long-term data sets, exceeding the duration of many sampling programs, are needed to detect trends in most aspects of habitat condition.