Antibiotics are widely used in livestock production, and up to 90% are excreted unmetabolized, which maintains selective pressure on manure-associated bacteria. Application of manure as a soil amendment to farm fields can introduce antibiotic residues, resistant bacteria, and antimicrobial resistance genes (ARGs) into adjacent streams, serving as potential sources of resistance to humans and the environment. While previous studies have documented that ARGs are frequently found in agricultural streams, mechanisms controlling their fate and transport remain poorly understood. We hypothesized that animal feeding operation (AFO) inputs would elevate downstream ARG loads, with highest values during spring and fall manure-application periods. Over 24 months, we sampled upstream and at four sites downstream of an AFO and examined relationships between the concentrations of four ARGs, dissolved nutrients, and physiochemical parameters. Finally, we developed a simplified hydrological model to characterize reach-scale ARG transport patterns. The AFO input significantly increased stream ARG loads during fall, winter and spring (estimated marginal means [EMM], all p<0.05). We also predicted that discharge and manure-associated drivers (e.g., ammonium, soluble reactive phosphorus [SRP], turbidity, and conductivity) would correlate with ARGs, and found that SRP and turbidity explained the greatest variation in ARG concentrations at both upstream and downstream sites, correlating positively with all four ARG targets at the downstream sites. For all seasons, ARG concentrations positively correlated with ammonium (Spearman’s ρ=0.49-0.65, p<0.05), and SRP (ρ=0.63-0.84, p<0.01), and during winter, were positively correlated with discharge (ρ=0.45-0.63, p < 0.01), suggesting that runoff due to increased precipitation drives manure-derived inputs. Summer ARG concentrations were negatively associated with dissolved oxygen (ρ=-0.66 to -0.78, p<0.001) and positively with temperature (ρ=0.49-0.68, p<0.01), potentially reflecting increased in-stream microbial activity. Across 60 reach-scale model fits, 31 indicated removal-dominated ARG dynamics with lateral inputs comparable to stream concentrations. An additional 26 runs supported a dilution+removal scenario with diffuse inputs, including 18 with net downstream enrichment and 8 where inputs were offset by removal. These results demonstrate that AFOs can substantially elevate stream ARG loads and that hydrology can influence downstream persistence. Optimizing manure application timing relative to seasonal hydrology could reduce ARG dissemination into streams.