Numerical models are of fundamental usage for estuarine and coastal sciences. Although numerical simulations are widely applied, analyzing and improving them are often challenging tasks given their large volume and huge parameter space. In this study, a novel data‐driven framework is introduced to study the Minjiang River Plume (MJRP). The framework combines Self‐Organizing Map (SOM) clustering with a Hidden Markov Model (HMM). A three‐dimensional Regional Ocean Model System for MJRP is first configurated with realistic atmospheric, oceanic, and riverine forcings. By applying SOM clustering to the modeled sea surface salinity (SSS) with ∼2,000 2‐day averaged records from 2010 to 2020, we identify six major patterns of MJRP. Each pattern exhibits distinct circulation and plume structures. These MJRP patterns contain not only seasonal signals, but also rich short‐term variabilities driven by the riverine inputs and oceanic dynamics. Then, the SOM‐HMM method was applied to predict the future of the hidden state (i.e., patterns of MJRP) from the observable states (wind and river runoff). With a hypothetic SSS product from a geostationary satellite as the ground truth, we show that the SOM‐HMM method can predict MJRP patterns considerably high prediction accuracy and computational efficiency. Further, these patterns were translated back to SSS with high forecast skills. Combining a conventional numerical model with a data‐driven method, this approach can be promisingly applied in the short‐term marine forecast to support the utilization and management of other estuaries.