In an era marked by unprecedented anthropogenic change, marine systems are increasingly subjected to interconnected and dynamic external stressors, which profoundly reshape the behavior and resilience of marine ecological components. Nevertheless, despite widespread recognition of the significance of stressor interactions, there persist notable knowledge deficits in quantifying their interactions and the specific biological consequences that result. To bridge this crucial gap, this research detected and examined the causal relationships between five key exogenous stressors in a complex estuarine ecosystem. Furthermore, a Bayesian Hierarchical Spatio-temporal modeling framework was proposed to quantitatively evaluate the distinct, interactive, and globally sensitive effects of multiple stressors on the population dynamics of a crucial fish species Harpadon nehereus. The results showed that interactions were detected between fisheries pressure (FP), the Pacific Decadal Oscillation index (PDO), runoff volume (RV), and sediment load (SL), with five of these interactions producing significant synergistic effects on H. nehereus biomass. The SL*PDO and RV*PDO interactions had positive synergistic effects, albeit through differing processes. The former interaction amplified the individual effects of each stressor, while the latter reversed the direction of the original impact. Indeed overall, the synergistic effect of multiple stressors was not favorable, with FP in particular posing the greatest threat to H. nehereus population. This threat was more pronounced at high SL or negative PDO phases. Therefore, local management efforts aimed at addressing multiple stressors and protecting resources should consider the findings. Additionally, although the velocity of climate change (VoCC) failed to produce significant interactions, changes in this stressor had the most sensitive impacts on the response of H. nehereus population. This research strives to enhance the dimensionality, generalizability, and flexibility of the quantification framework for marine multi-stressor interactions, aiming to foster broader research collaboration and jointly tackle the intricate pressures facing marine ecosystems.