The prevalence of antimicrobial resistance (AR) is a pressing global health crisis that threatens to undermine the effectiveness of antibiotics and other antimicrobial agents. The prevalent use of antibiotics in animal husbandry, and subsequent application of manure to croplands, can lead to the persistence of antimicrobial resistance genes (ARGs) in aquatic ecosystems in agricultural landscapes. Seasonal leaf litter inputs provide a significant source of allochthonous carbon to fluvial networks and their biofilms can serve as a sink for various pollutants, like ARGs, through sorption and biodegradation processes. We currently lack an understanding of the ecological factors, including allochthonous inputs and biofilm colonization, that influence the transport of ARGs in streams. To explore this, we quantified water column removal rates of two ARGs (tetracycline-resistant tetQ and tetW) using replicated recirculating mesocosms amended with uncolonized leaf litter, biofilm-colonized leaf litter, dissolved organic carbon (DOC) leached from leaves, and mesocosms without leaf litter (as controls). To quantify ARG removal rates, we added a cow manure slurry and then collected water samples at 0.33, 4, 8, 16, and 24 hr, which we filtered immediately, extracted, and analyzed for ARGs using digital PCR. For tetQ, removal rates (as k, in h-1) were k=0.36, 0.29, 0.35, and 0.12 h-1 for uncolonized-leaves, colonized-leaves, DOC, and controls, respectively. For tetW, removal rates were k=0.23, 0.27, 0.25, and 0.17 h-1 for uncolonized-leaves, colonized-leaves, DOC, and controls, respectively. Surprisingly, the two tetracycline-resistant targets responded uniquely to the experimental treatments. For tetQ, uncolonized-leaves, colonized-leaves, and DOC all significantly increased removal rates (ANOVA; p=0.003), but rates were not distinct from each other. For tetW, there was no treatment-effect on removal rates (ANOVA; p=0.159), suggesting that ARG removal is target-specific. This research will enhance our forecasting capabilities regarding ARG transport in streams, and will inform effective strategies to curtail the spread of AR.