Based on a survey conducted from June to July 2013, aragonite saturation state variation and control in the river-dominated marginal BoHai and Yellow seas were investigated. Surface water $Ømega$arag ranged from 2.0–3.8, whereas subsurface water $Ømega$arag was generally lower than 2.0. Temperature changes had a strong influence on $Ømega$arag through induced CO2 solubility changes in seawater. Riverine freshwater input decreased $Ømega$arag in the Changjiang and Yalu river estuaries, but induced higher $Ømega$arag in the Yellow River estuary. Biological processes had opposite effects on $Ømega$arag, whereby elevated biological production led to the highest $Ømega$arag in the South Yellow Sea surface water, whereas net community respiration/remineralization induced low $Ømega$arag in subsurface water. Stratification affected the level and scale of low $Ømega$arag in subsurface water. By the year 2100, surface water with $Ømega$arag \textgreater 2.0 will disappear except for the Yellow River estuary, and most of the subsurface water will develop substantial aragonite undersaturation.