We have used a dynamic hydrologic network model, coupled with a transient storage zone solute transport model, to simulate dissolved nutrient retention processes during transient flow events at the channel network scale. We explored several scenarios with a combination of rainfall variability, and biological and geomorphic characteristics of the catchment, to understand the dominant factors that control the transport of dissolved nutrients (e.g., nitrate) along channel networks. While much experimental work has focused on studying nutrient retention during base flow periods in headwater streams, our model-based theoretical analyses, for the given parameter combinations used, suggest that high-flow periods can contribute substantially to overall nutrient retention, and that bulk nutrient retention is greater in larger rivers compared to headwaters. The relative efficiencies of nutrient retention during high- and low-flow periods vary due to changes in the relative sizes of the main channel and transient storage zones, as well as due to differences in the relative strengths of the various nutrient retention mechanisms operating in both zones. Our results also indicate that nutrient retention efficiency at all spatial scales of observation has strong dependence on within-year variability of streamflow (e.g., frequency and duration of high and low flows), as well as on the relative magnitudes of the coefficients that govern biogeochemical uptake processes: the more variable the streamflow, the greater the export of nutrients. Despite limitations of the model parameterizations, our results suggest that increased attention must be paid to field observations of the interactions between process hydrology and nutrient transport and reaction processes at a range of scales to assist with extrapolation of understandings and estimates gained from site-specific studies to ungauged basins across gradients in climate, human impacts, and landscape characteristics.