<p>Calcareous fens are groundwater-dependent peatlands that regulate nitrogen (N) availability between aquifers and surface waters, yet their functioning under legacy nitrate (NO₃⁻-N) groundwater contamination remains poorly understood. This study investigated spatial and temporal patterns of NO₃⁻-N at Greywell Fen, a chalk aquifer-fed system in southeast England subject to decades of agricultural N enrichment and groundwater abstraction. Two to four week hydrochemical sampling at 45 locations revealed spatial NO₃⁻-N heterogeneity controlled by groundwater discharge zones. Hierarchical Cluster Analysis identified three hydrochemical signatures: 78% of pore waters exhibited depleted NO₃⁻-N (&lt; 1&#xa0;mg NO₃⁻-N L⁻¹) with elevated dissolved organic carbon (DOC) and iron (Fe^2+/3+), while 22% maintained high NO₃⁻-N (1.37–6.86&#xa0;mg NO₃⁻-N L⁻¹) and Ca²⁺ concentrations. Principal Component Analysis confirmed transport-dominated zones (high NO₃⁻-N, Ca²⁺) versus reaction-dominated zones (high Fe^2+/3+, DOC). Strong negative correlations between NO₃⁻-N and the Mg²⁺:Ca²⁺ ratio (ρ = -0.69) revealed residence time controls on N transformation. Regression and relative importance analysis identified DOC and Fe^2+/3+ as dominant controls on pore water NO⁻₃-N (91.4% of variance), with Mg²⁺:Ca²⁺ contributing only 8.6%, demonstrating that groundwater discharge influences pore water NO^-₃-N indirectly through redox conditions. A heterogeneous clay layer likely explains spatial distribution by partitioning the fen from NO⁻₃-N-enriched groundwater; high NO₃⁻-N areas emerge at discrete discharge zones, where the clay is thinner. Temporal concentration stability, maintained by consistent groundwater inflows and floating fen characteristics, confirms that hydrogeomorphic controls dominate over seasonal conditions. These findings challenge hydrological connectivity assumptions in groundwater-dependent ecosystems and suggest zone-based management approaches over uniform strategies.</p> Graphical Abstract <p></p>