In-stream nitrogen processing in the Mississippi River has been suggested as one mechanism to reduce coastal eutrophication in the Gulf of Mexico. Aquatic macrophytes in river channels and flood plain lakes have the potential to temporarily remove large quantities of nitrogen through assimilation both by themselves and by the attached epiphyton. In addition, rooted macrophytes act as oxygen pumps, creating aerobic microsites around their roots where coupled nitrification-denitrification can occur. We used in situ 15 N-NO 3 -tracer mesocosm experiments to measure nitrate assimilation rates for macrophytes, epiphyton, and microbial fauna in the sediment in Third Lake, a backwater lake of the upper Mississippi River during June and July 2005. We measured assimilation over a range of nitrate concentrations and estimated a nitrate mass balance for Third Lake. Macrophytes assimilated the most nitrate (29.5 mg N m -2 d -1 ) followed by sediment microbes (14.4 mg N m -2 d -1 ) and epiphytes (5.7 mg N m -2 d -1 ) . Assimilation accounted for 6.8% in June and 18.6% in July of total nitrate loss in the control chambers. However, denitrification (292.4 mg N m -2 d -1 ) is estimated to account for the majority (82%) of the nitrate loss. Assimilation and denitrification rates generally increased with increasing nitrate concentration but denitrification rates plateaued at about 5 mg N L -1 . This suggests that backwaters have the potential to remove a relatively high amount of nitrate but will likely become saturated if the load becomes too large.

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Long-term trends in tributaries provide valuable information about temporal changes in inputs of nutrients and sediments to large rivers. Data collected from 1991 to 2014 were used to investigate trends in total nitrogen (TN), total phosphorus (TP), nitrate (NO3-N), soluble-reactive P (SRP), and total suspended solids (TSS) in the following six tributaries of the upper Mississippi River: Cannon (CaR; Minnesota (MN)), Maquoketa (MR; Iowa (IA)), Wapsipinicon (WR; IA), Cuivre (CuR; Missouri (MO)), Chippewa (ChR; Wisconsin (WI)), and Black (BR; WI) rivers. Weighted regression on time discharge and season was used to statistically remove effects of random variation in discharge from estimated trends in flow-normalized concentrations and flux. Concentration and flux of TSS declined in all six rivers. Concentration of P declined in four of the rivers, and P flux declined in five rivers. Concentration and flux of N exhibited small changes relative to TP. TN concentration and flux did not change substantially in four of the rivers and decreased in two (ChR, CuR). Nitrate concentration and flux increased in three rivers (ChR, BR, CaR) and remained relatively constant in the other three rivers. General declines in P and TSS suggest that improvements in agricultural land management, such as the adoption of conservation tillage and enrollment of vulnerable acreage into the Conservation Reserve Program, may have reduced surface runoff; similar reductions in N were not observed.

Despite much research and investment into understanding and managing nutrients across agricultural landscapes, nutrient runoff to freshwater ecosystems is still a major concern. We argue there is currently a disconnect between the management of watershed surfaces (agricultural landscape) and river networks (riverine landscape). These landscapes are commonly managed separately, but there is limited cohesiveness between agricultural landscape-focused research and river science, despite similar end goals. Interdisciplinary research into stream networks that drain agricultural landscapes is expanding but is fraught with problems. Conceptual frameworks are useful tools to order phenomena, reveal patterns and processes, and in interdisciplinary river science, enable the joining of multiple areas of understanding into a single conceptual-empirical structure. We present a framework for the interdisciplinary study and management of agricultural and riverine landscapes. The framework includes components of an ecosystems approach to the study of catchment-stream networks, resilience thinking, and strategic adaptive management. Application of the framework is illustrated through a study of the Fox Basin in Wisconsin, USA. To fully realize the goal of nutrient reduction in the basin, we suggest that greater emphasis is needed on where best management practices (BMPs) are used within the spatial context of the combined watershed-stream network system, including BMPs within the river channel. Targeted placement of BMPs throughout the riverine landscape would increase the overall buffering capacity of the system to nutrient runoff and thus its resilience to current and future disturbances.