Deoxygenation in marine ecosystems has received increasing attention. The variation of dissolved organic matter (DOM) during deoxygenation has been investigated in hypoxic and anoxic waters in coastal seas and open oceans. In the present study, the dynamics of DOM were investigated during summertime deoxygenation in the bottom water of the shallow coastal Bohai Sea, China. Dissolved organic carbon (DOC), chromophoric and humic-like fluorescent DOM (CDOM and FDOM) gradually increased in the bottom water during summer, which was mainly induced by biological activities in the water column and/or the surface sediment. The estimated net accumulation rates of DOC, CDOM and humic-like FDOM from June to early August in the bottom water were 0.11 ± 0.04 µmol L⁻¹ d⁻¹, 0.002 ± 0.0002 m⁻¹ d⁻¹ and 0.0004 ± 0.0001 R.U. d⁻¹, respectively. Moreover, the ratio of DOC to CO₂ accumulations was 0.08 in this duration in the bottom water. Compared with DOM in the bottom water prior to deoxygenation, the newly accumulated DOC contained more CDOM and humic-like FDOM that are considered to be microbially refractory.