Rivers across the globe experience and respond to changes within the riparian corridor. Disturbance of the riparian corridor can affect warmwater, intermediate, and coldwater streams, which can negatively influence instream physical structure and biological communities. This study focused on assessing the influence of the riparian habitat on instream structure within the Whitewater River, a coldwater stream system within an agricultural watershed in southeastern Minnesota, USA. To understand the influence of the riparian zone on the physical instream habitat, twenty variables (riparian, n = 9; instream, n = 11) were measured at 57 sites across three forks of the Whitewater using a transect method every 10 m across a 150 m reach. We used a modified Wentworth scale approach to assess coarse and fine substrates to describe habitat conditions. Canonical correlation detected significant associations between riparian and instream variables across the river forks, and indicated that wider riparian buffers, more bank grass and shrubs, longer overhanging vegetation, limited bare soil, and more rocks on banks were significantly associated with increased instream cover, high levels of coarse substrates with reduced embeddedness, increased pool habitats, and reduced fine sediments. In contrast, excessive fine sediments, lack of riffle habitat, reduced coarse substrates, and high width to depth ratios indicative of an impaired instream habitat were associated with narrow riparian buffers and high percentages of bare soil on banks. Riparian corridors have the capacity to enhance and protect physical instream habitats and overall ecosystem health when managed properly. Wide, grassy riparian corridors with stable banks, overhanging vegetation, and limited shade from trees should protect and/or enhance the instream physical habitat, providing the structural diversity favored by aquatic communities. We recommend revising the current Best Management Practices to include monitoring for impairments in the riparia, while promoting and developing good land stewardship with private landowners which can be effective in improving river ecosystems in agricultural settings.