Electromagnetic field (EMF) treatment has emerged as a promising approach for scaling control due to its cost-effectiveness, simplicity, and low energy consumption. However, there is a limited understanding of the mechanisms by which applied EMF impacts mineral scaling in reverse osmosis (RO) systems. This has led to inconclusive and varied results and uncertainties regarding its effectiveness. This study elucidates the impacts of EMF on homogenous and heterogeneous nucleation and membrane performance during RO desalination of different feedwaters. Our results reveal that EMF exhibits greater efficacy in treating near-saturated water (SI∼0), especially when coupled with extended hydraulic flushing (HF). For saturated brackish water desalination, heterogeneous scaling predominantly occurs on membrane surfaces, with the effectiveness of EMF in inhibiting scaling primarily attributed to the hydration effect. In supersaturated solutions, EMF promotes bulk precipitation due to the magnetohydrodynamic effect, quickly blocking membrane pores. Thus, when the saturation reaches a certain high level during RO desalination, magnetohydrodynamic EMF effects can accelerate flux decline caused by homogeneous scaling. This work provides an efficient method for predicting EMF efficiency, emphasizing the importance of saturation conditions and HF cleaning duration in determining membrane performance, suggesting these show promise for improving undersaturated or near-saturated feedwater desalination via RO.