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Algae and aquatic plants support river food webs through in-situ primary production. However, gross primary production (GPP) and ecosystem respiration (ER) are rarely evaluated in the context of river management or habitat restoration. We estimated daily GPP and ER during 2 growing seasons for 7 reaches in the Kootenai River and 1 reach in the Elk River, spanning 290 river km across British Columbia, Canada, and Montana and Idaho, USA. We characterized responses of GPP and ER to river management, including reaches with unregulated flow, regulated flow, nutrient addition, and habitat restoration. Downstream GPP and ER generally increased after changes in river management, and higher management intensity led to greater increases. GPP and ER followed a seasonal pattern with low initial values in spring, elevated values in mid-summer, and a return to low values in late summer and autumn. Timing and duration of the elevated period for GPP and ER also differed among reaches following changes in river management. Our results suggest that river management affects GPP and ER, likely through reducing turbidity and the frequency and magnitude of extreme flow events, nutrient additions, and enhanced floodplain connectivity, thereby altering the timing and amount of autochthonous carbon available to the food web.

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