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Macrophytes provide essential ecosystem services in lowland streams, including nutrient uptake that can reduce downstream transport to vulnerable coastal areas. Despite that, to ensure water conveyance and effective run off from agricultural fields, aquatic plant biomass is removed regularly in many European streams (i.e. weed cutting practices). However, the impacts of weed cutting on stream ecosystem processes are not yet well documented. Here, we studied the effect of weed cutting on nutrient retention and ecosystem metabolism in three lowland streams with contrasting dominant vegetation communities (submergent and emergent plants) during summer in Denmark. Our results showed a decrease in nutrient retention; uptake velocity of ammonium decreased 34–77 % and of phosphate decreased 50–77 %. Ecosystem metabolic rates also decreased after weed cutting, both in gross primary production (9 %, 60 % and 85 %) and respiration (47 %, 69 % and 76 %). The effects of weed cutting on these ecosystem processes prevailed three weeks after the cutting occurred. Understanding the effects of weed cutting on stream ecosystem functioning can improve nature-based management strategies to control eutrophication of downstream coastal areas. [Display omitted] • Stream gross primary production and respiration decreased after weed cutting. • Nutrient retention decreased after weed cutting, but only partially attributed to weed cutting. • The effects of weed cutting prevailed after three weeks. [ABSTRACT FROM AUTHOR]