This project aimed to provide the client, the Huron River Watershed Council (HRWC), with a framework for assessing flow alteration and its impact on the biological community of the Huron River. Within the watershed, analyses on annual, monthly, daily and sub-daily hydrological data, precipitation, land cover change, and fish and benthic invertebrate communities were conducted. Most hydrologic parameters concerning flow volume demonstrated an upward or non-changing pattern for the most recent 100 years. The base flow gradually increased, while the reversal number gradually decreased, suggesting a more stable flow regime. In terms of daily and sub-daily flow regime, the largest flashiness was demonstrated by the gauge near Ann Arbor, which could be the result of dam regulation in the upstream region. A strong correlation was found between precipitation and flow discharge. Both precipitation and flow discharge showed a similar increasing trend, while the runoff coefficient did not change significantly over time. This result implies that the increase in precipitation is a major driver of flow increase. With the current climate change trend, more water is expected in the river. Furthermore, increased impervious land in the watershed has resulted in more runoff from rainfall events and led to higher flashiness in the river. The corresponding increase of fine substrate and pollutants has also had a negative impact on stream habitats for benthic macroinvertebrates. At sample sites along the river, fish preferences (e.g. water temperature, stream size, substrate type, etc.) defined two guilds: riverine and impoundment. In impoundment environments, a high percentage of the sample taxa were: game fish, tolerant species, substrate generalists, piscivores and had preferences for larger rivers and slow current velocity. Conversely, in riverine environments, a high percentage of the sample taxa were: darters, intolerant species, insectivores, and had preferences for rock or gravel substrate and wider range of current velocities. Along the Huron River main stem, a habitat suitability model was used to predict expected fish communities at a given site and then compared to sampled fish communities. Fish communities around Ann Arbor and Ypsilanti were found to not be representative of model communities for the river type, temperature, and size. Present fish communities preferred a flow range with a significantly higher upper bound. An Adverse Resource Impact occurs in Ann Arbor at a low flow of around 45 cfs and in Ypsilanti at around 51 cfs. This serves as the critical low flow value for management purposes. Ann Arbor has the highest amount of historic ARI occurrences throughout the Huron River indicating that it is necessary to prioritize dam operations associated with this site.