Water from different sources generally contains different kinds of suspended particles, which introduces the challenge of how to control physical clogging during managed aquifer recharge (MAR). Suspended solid concentration (SS) and turbidity (NTU) are widely recognized as indicators of physical clogging potential. The aims of this study were to examine the degree of physical clogging caused by organic and inorganic suspended particles and elaborate the different mechanisms that controlled clogging under specific SS and NTU conditions. Column experiments were performed by continuous suspended particle injection through a saturated porous medium under stable physicochemical and hydrodynamic conditions. Three sets of transport tests were carried out. One test was conducted with chlorinated-secondary wastewater (CSW), which SS was 17.59 ± 0.44 mg L−1 corresponding to 3.09 ± 0.05 NTU. The other two tests were silica-particle wastewater (SPW) with the same SS (1.73 ± 0.03 NTU) and the same NTU (29.21 ± 0.57 mg L−1 SS) as the CSW, abbreviated to SPW-SS and SPW-NTU, respectively. The particle breakthrough curves (BTCs), spatial deposition profiles, and variations in hydraulic conductivity were measured. The transport model, DLVO theory, and O’Melia and Ali clogging model were applied to explain the mechanisms of physical clogging in different systems. The retention of inorganic particles was greater than that of organic particles; 56.02% of organic particles were retained in CSW, while 87.62 and 86.36% of inorganic particles were retained in SPW-SS and SPW-NTU, respectively. The distribution of organic particles was less uniform than that of inorganic particles. However, the variation of the relative hydraulic conductivity (K/K0) was more significant for organic particles than for inorganic particles, with decreased by just 1.80 ± 0.64% in SPW-SS and 4.03 ± 1.64% in SPW-NTU, but decreased by 85.86 ± 1.22% in CSW. This study explained the results with the support of classical models and the DLVO theory. The physicochemical characteristics of suspended particles determined whether and how physical clogging occurred. Suspended particles with different properties follow different transport-deposition processes and have different tendencies to cause physical clogging. Especially for organic particles, clogging degree is quite noticeable. Our results imply that the same SS and NTU threshold values cannot be applied to different types of source water during recharge to prevent physical clogging, even in the same controlled environmental conditions. Physicochemical characteristics of suspended particles need to be considered when developing physical clogging indicators.