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Abstract Marine dissolved organic carbon and nitrogen (DOC and DON) are major global carbon and nutrient reservoirs, and their characterization relies on extraction methods for preconcentration and salt removal. Existing methods optimize for capturing and describing DOC. Here, we report an optimized analytical strategy to recover marine DON for subsequent molecular characterization. Retention efficiencies between 5% and 95% are reported for seven solid phase extraction (SPE) sorbents, with PPL recovering 23% of marine DON compared to 95% recovered with C₁₈. Additional comparisons of the effect of varying sample volumes and elution speed, and the resulting molecular composition of DON extracts, were investigated using C₁₈and PPL sorbents. Sample volumes > 200 mL decreased DON retention efficiency independent of SPE sorbent, and gravity elution recovered 1.7‐ to 4.2‐fold more DON compared to vacuum elution. Characterization of extracted DON by negative‐ion electrospray ionization Fourier transform‐ion cyclotron resonance mass spectrometry (FT‐ICR MS) highlights compositional differences between DON species recovered by each method. DON isolated with optimized methods includes low molecular weight (< 600 Da) peptide‐like compounds with low O:C ratios (0.2 to 0.5) that are not detected by other SPE sorbents (e.g., PPL). The majority of additional DON isolated with this approach was undetectable by direct infusion negative mode FT‐ICR MS analysis.