River systems with impoundments are expected to experience greater nutrient removal as a consequence of enhanced nitrogen (N) loss by denitrification, settling and burial of phosphorus (P), and longer residence times of water relative to a free-flowing river. We evaluated the magnitude of N and P removal across stream reaches and impoundments, including annual and seasonal trends, in two southeastern Michigan rivers that differ in their degree of impoundment and watershed land use patterns. All nutrient fraction concentrations remained statistically unchanged across stream reaches of 2–3 km in length, but dissolved oxygen and pH increased. Impoundment outlets exhibited increases in water temperature and decreases in conductivity, TP, TN, TDP, SRP, TDN, and NO3-N relative to inflowing water. A nutrient load mass balance showed that two connected impoundments removed 18 and 32% of the annual river loads of TN and TP, respectively. Removal rates were seasonably variable, with TP removal most pronounced during winter months when the impoundment received episodic high P loads. Conversely, TN removal was greatest during summer and autumn months when impoundments were stratified and water temperatures were elevated. Strong seasonal differences in N and P transport through the impoundments demonstrated the capacity of impoundments to dramatically alter the timing and stoichiometry of downstream nutrient export. These seasonal differences also highlight the need to consider the entire annual cycle when estimating surface water nutrient dynamics or designing management plans for nutrient abatement.