The upper Marys provides habitat for coastal cutthroat trout, Pacific lamprey and sand rollers. This upper reach of the Marys River Watershed has a legacy of extensive beaver impoundments that provided water storage to supply downstream flows late into the season.

Middle Marys River extends from Muddy Creek in Corvallis to Blakesley Creek in Wren. Steep cliffs and bedrock intrusions occur in the uppermost reach of middle Marys. Below Woods Creek, the river meanders slowly along a relatively flat course, cutting a deep channel through deep silt deposits.