Clay is widely encountered in nature and directly influences seepage behaviors, exerting a crucial impact on engineering applications. Under low hydraulic gradients, seepage behaviors have been observed to deviate from Darcy’s law, displaying a non-linear trend. However, the impacts of clay content on non-linear seepage behavior and its pore-scale mechanisms to date remain unclear. In this study, constant-head seepage experiments were conducted in sand–clay porous media under various hydraulic gradients. Low-field nuclear magnetic resonance (LF-NMR) technology was utilized to monitor the bound-water and free-water contents of sand–clay porous media under different seepage states. The results show a threshold hydraulic gradient (i₀) below which there is no flow, and a critical hydraulic gradient (i_cr) below which the relationship between the hydraulic gradient (i) and seepage velocity (v) is non-linear. Both hydraulic gradients increased with clay content. Moreover, the transformation between bound water and free water was observed during the seepage-state evolution (no flow to pre-Darcy or pre-Darcy to Darcy). As the hydraulic gradient reached the i₀, the pore water pressure gradually overcame the adsorption force of the bound-water film, reducing the thickness of the bound-water film, and causing non-linear seepage behavior. When i₀ < i < i_cr, the enlarging hydraulic gradient triggers the thinning of bound water and enhances the fluidity of pore water. Moreover, the increasing clay content augments the bound-water content required for the seepage state’s change.