The objective of this study was to investigate the diagenetic alteration of sediment organic matter (OM) in the upper Pearl River Estuary. Sediment analyses were conducted for three size fractions of OM, including coarse particulate OM (CPOM), fine particulate OM (FPOM), and ultrafiltered dissolved OM (UDOM). Results showed that the highest and lowest carbon (C): nitrogen (N) ratios were in CPOM and UDOM, respectively, indicating that CPOM was relatively enriched in organic C. The highest average total N content in the FPOM fraction showed that FPOM was enriched in N-containing molecules. Our study showed that the "size-reactivity continuum" model was applicable to sediment particulate and dissolved OM. Distributions of amino acids and their D-isomers among the sediment fractions indicated that the amino acid-based diagenetic index, C:N ratio, and percentage of total N represented by total hydrolysable amino acids could be used as diagenetic indicators. Furthermore, the diagenetic state of sediment OM could also be characterized by C- and N-normalized yields of total D-amino acids, and C- and N-normalized yields of D-alanine, D-glutamic acid, and D-serine.