The subterranean estuary (STE) has been recognised as a reactive biogeochemical zone at the groundwater–seawater interface in coastal areas. In this study, we collected sediments from different seasons (April 2021 [storm season) and September 2021 [dry season]) from Mobile Bay, USA. Shallow sediment cores (up to 2 m) were recovered using a Geoprobe coring system (Model 5410, Geoprobe Systems, Inc.). We conducted controlled laboratory experiments using these sediments and subjected them to various nitrate inputs (Storm/Dry 2-4, GW1-2), saline solutions (Storm/Dry 5-6, SW1-2), and incubation times (Storm/Dry 7-8). We measured (1) inorganic nutrients (nitrate, nitrite, ammonium, phosphate), (2) dissolved organic carbon (DOC), and (3) dissolved organic nitrogen (DON) concentration. Dissolved organic matter (DOM) quality was analyzed with Fourier-transform ion cyclotron resonance mass spectrometry.