We monitor infiltration at multiple scales during managed aquifer recharge with desalinated seawater in an infiltration pond, while groundwater recharge is evaluated by simplified and numerical models. We found that pond-surface clogging is negated by the high-quality desalinated seawater or negligible compared to the low-permeability layers of the unsaturated zone. We show that a numerical model with a 1-D representative sediment profile is able to capture infiltration and recharge dynamics.