Excess nitrogen (N) export from lowland artificial watersheds (polders) is often assumed to be a major contributor to the cultural eutrophication of downstream aquatic ecosystems. However, the complex transport processes characterizing lowland areas pose significant challenges in accurately quantifying their actual role. In this study, we developed a dynamic model to track N sources and transport pathways in lowland polders. The model is able to accommodate all the unique characteristics of polder dynamics, including artificial drainage, and interactions among surface water, groundwater and soil water. Our model was calibrated and validated against water level data and nitrogen concentrations measured in a lowland polder (Polder Jian) in China during the 2014–2016 period. Model performance was satisfactory with an R² value of 0.55 and an NS value of 0.53 for total N concentrations. The characterization of the various components of water budget and N cycle derived by the model was on par with local empirical estimates. N export from Polder Jian was approximately 57 kg ha⁻¹ yr⁻¹ and was distinctly higher than values reported from nearby non-polder areas. The largest fraction of N export stemmed from seepage. To our knowledge, this is the first dynamic model to quantify N export from a watershed with artificial drainage network and can be used to design remedial measures of ecosystem degradation.