Nutrient dynamics in karst agroecosystems remain poorly understood, in part due to limited long-term nested datasets that can discriminate upland and in-stream processes. We present a 10-year dataset from a karst watershed in the Inner-Bluegrass Region of central Kentucky, consisting of nitrate (nitrate-N [NO 3 − ]), dissolved reactive phosphorus (DRP), total organic carbon (TOC), and total ammoniacal-N (TAN) measurements at nested spring and stream sites as well as flowrate at the watershed outlet. Hydrograph separation techniques were coupled with multiple linear regression and Empirical Mode Decomposition time-series analysis to determine significance of seasonal processes and to generate continuous estimates of nutrient pathway loadings. Further, we used model results of benthic algae growth and decomposition dynamics from a nearby watershed to assess if transient storage in algal biomass could explain differences in spring and downstream watershed nutrient loading. Results highlight statistically significant seasonality for all nutrients at stream sites, but only for NO 3 − at springs with longitudinal variability showing significant decreases occurring from spring to stream sites for NO 3 − and DRP, and significant increases for TOC and TAN. Pathway loading analysis highlighted the importance of slow flow pathways to source approximately 70% of DRP and 80% of NO 3 − . Results for in-stream dynamics suggest that benthic autotroph dynamics can explain summer deviations for TOC, TAN, and DRP but not NO 3 − . Regarding upland dynamics, our findings agree well with existing perceptions in karst for N pathways and upland source seasonality but deviate from perceptions that karst conduits are retentive of P, reflecting the limited buffering capacity of the soil profile and conduit sediments in the Inner-Bluegrass. Regarding in-stream fate, our findings highlighted the significance of seasonally driven nutrient processing in the bedrock-controlled streambed to influence nutrient fluxes at the watershed outlet. Contrary to existing perceptions, we found high N attenuation and an unexplained NO 3 − sink in the bedrock stream, leading us to postulate that floating macrophytes facilitate high rates of denitrification. KEYWORDS bedrock stream, hydrologic pathways, in-stream fate, karst agroecosystem watershed, nutrient loadings, time-series analysis