Sorption of organic compounds by coastal marine sediments is strongly affected by dry–wet cycling. In this study, we determined how drying (and rewetting) sediment affected the decomposition rate of organic matter under both oxic and anoxic conditions, and how sorption changed with decomposition. Organic matter decomposition showed distinct patterns in dried, rewetted sediments compared to those that had never been dried, based on a comparison of ammonium production rates, OC/N ratios and total hydrolyzable amino acid (THAA) loss rates. Net ammonium production rates were 29 (oxic) and 44 μM/d (anoxic) in dried, rewetted sediment and 4 (oxic) and 13 μM/d (anoxic) in wet, never-dried sediment, indicating that a fraction of labile organic compounds like protein, was preferentially decomposed after a dry–wet cycle. The input of fresh organic matter from benthic fauna and microbes killed by the drying process may partially explain the faster remineralization rates in rewetted sediment. The decomposed organic matter in dried sediment might also come from resynthesized microbial biomass or its related byproducts, with low C/N ratios. Based on comparisons between wet and dried sediments, we hypothesize that sedimentary organic matter (SOM) can assemble into 3D structures that play a significant role in the remineralization pathways of SOM. Drying not only changes the lability of salt marsh SOM, either through exposed proteinaceous matter or resynthesized matter by microbes, but also its sorption capacity. Lysine sorption was used as a probe to test the structural changes of sediment during the incubation. Lysine sorption in both wet and dried sediment remained relatively constant when sediments were incubated under anoxic conditions, although there was much stronger sorption in continuously wet sediment than in dried–rewetted sediment. Under oxic conditions, lysine sorption in both dried and wet sediment decreased dramatically after a one-month incubation, and the pH in these samples also decreased accordingly, suggesting that sulfide or ammonium might be oxidized to strong acids (H2SO4 and HNO3) that decrease lysine sorption. Overall, the structure of dried sediment did not appear to be reconstituted after 3-months of laboratory incubation.