The effects of timber harvest practices and climate change have altered forest ecosystems in southeast Alaska. However, quantification of patterns and trends in stream habitats associated with these forests is limited owing to a paucity of data available in remote watersheds. Here, we analyzed a 30-year dataset from southeast Alaska's Tongass National Forest to understand how these factors shape stream habitats. First, we examined differences between broad management classes (i.e., harvested and non-harvested) that have been used to guide stream channel restoration goals. Second, we assessed associations between intrinsic landscape characteristics, watershed management, and timber harvest legacies on aquatic habitat metrics. And third, we examined trends in stream habitat metrics over the duration of the dataset to anticipate future management challenges for these systems. Small effect sizes for some harvest-related predictors suggest that some stream habitat metrics, such as pool densities, are less responsive than others, and management practices such as protecting riparian buffers as well as post-harvest restoration may help conserve fish habitats. Large wood densities increased with time since harvest at sites harvested >50 years ago, indicating that multiple decades of post-harvest forest regrowth may contribute large wood to streams (possibly alder), but that it is not enough time for old-growth trees (e.g., spruce, Picea, or hemlock, Tsuga,), classified as key wood, to develop and be delivered to streams. The declining trend in key wood (i.e., the largest size class of wood) regardless of management history may reflect that pre-harvest legacy old-growth trees are declining along streams, with low replacement. The introduction of wood to maintain complex stream habitats may fill this gap until riparian stands again contribute structural key wood to streams. Trend analyses indicate an increasing spatial extent of undercut banks that may also be influenced by shifting hydrologic regimes under climate change.