The Minnesota River Headwaters watershed is comprised of the Little Minnesota River Watershed and several small watersheds that flow directly into the Minnesota River. The hydrologic Unit Code (HUC) watershed (i.e. 07020001) drains approximately 761 square miles of primarily agricultural land in west-central Minnesota, north-eastern South Dakota, and south-eastern North Dakota. The following report analyzes the hydrology, connectivity, and geomorphology components of the Minnesota River Headwaters watershed as well as general watershed characteristics. Historical gage data, stream crossing data, and applied fluvial geomorphology assessments were analyzed to characterize conditions of the watershed and find relationships to help understand water quality and biological impairments throughout the watershed. Analysis of land use within the watershed showed an increase in acres planted to corn and soybeans since the 1970’s, with a correlating decrease in acres planted to wheat and oats. Review of tile drainage records also showed an increase in both permit numbers issued, and average annual length of tile since the mid 2000’s. Precipitation data collected within the separate watersheds indicated variability in precipitation over time, but largely stayed within the 25-75th percentile range. When the same data were split into fourteen year increments, however, average annual precipitation has increased from north to south over time. Inflection points within the double mass curves for the Little Minnesota, Whetstone, and Yellow Bank rivers were identified in 1993, 1991, and 1984 respectively. Relationships in the double mass curves indicate the amount and timing of discharge per inch of precipitation has increased over time. General trends in cumulative annual precipitation before and after each inflection point identified an increase in fall, and decrease in summer, for both time periods in each watershed. Analysis of daily precipitation events for each watershed indicated an increase in frequency of larger daily precipitation periods for each of the watersheds. Cumulatively, monthly flow values have shown an increase in monthly average discharge volumes, and the number of days the one and a half year return interval flow has been met or exceeded has increased when assessing mean daily discharge. Longitudinal connectivity assessments within the watershed indicated a road crossing density of 3.01/mi2. High densities of road crossings were identified in the western portion of the watershed (i.e. along the Coteau des Prairies), while fewer crossings were identified in the eastern half. An extensive search of various databases identified fourteen longitudinal connectivity structures, ten that are longitudinal fish passage barriers, one that is a barrier at certain flows, and three that are not fish passage barriers at any flows. An additional assessment of longitudinal connectivity of riparian corridors was completed near the survey sites. The assessment found that nine survey locations had adequate riparian width, two had adequate width but were grazed pastures, two only had adequate width on one side, and one lacked adequate riparian corridor width altogether. Assessment of lateral connectivity at each of the survey locations indicated that one survey site was completely entrenched, two sites were moderately entrenched, and ten sites were in varying degrees of slight entrenchment. Survey assessment results indicated systemic issues within each of the watersheds. Channel stability at two survey sites was rated good, four sites were fair, and seven sites were poor. Survey sites included two ‘B’ channels, four ‘C’ channels, six ‘E’ channels, one ‘F’ channel, and one ‘G’ channel. Several sites appeared to be moving towards a state of channel succession through down cutting and widening, potentially resulting in different stream types in the future. Restoration and protection strategies within the Minnesota River Headwaters watershed should focus on system wide issues.