Managed aquifer recharge (MAR) is an emerging approach to enhancing water storage capacity, improving water supply security and countering groundwater overexploitation. However, physical clogging, i.e. accumulation of suspended organic and inorganic solids within a sediment matrix, can lead to a significant reduction of infiltration rates and present difficulties in the functioning of MAR infrastructure. Clogging and subsequent reduction in infiltration capacity are often quantified based on monitoring data or field investigations, rather than on forecasts. Existing predictive models require specific parameterisation, making an application to heterogeneous sites, or under changing conditions, difficult. Hence, a generalised understanding of how intrusive fine particles distribute over depth during water recharge cycles for typical MAR infiltration basin sediments is needed to predict clogging susceptibility and clogging patterns already in the planning phase and before operation of MAR schemes. The study will contribute to operational reliability, deduce optimised management practices, and, ideally, reduce maintenance efforts. To achieve this goal, data from different soil-column clogging experiments are reviewed and complemented with experiments to establish a generally valid relationship for the vertical distribution of intrusive fines under consideration of the primary porous media’s and intruding particles’ characteristics. Obtained results allow for quantification of the amount of particles retained at the surface of the porous media, i.e. formation of a filter cake, a description of the distribution of fines over depth, and total clogging depth. Finally, the findings are applied to a real MAR case study site to showcase the quantification of clogging effects on recharge rates.