Infiltration basins are increasingly used in urban areas for flood protection, groundwater recharge and storm water disposal. However, their operation is often affected by clogging, leading to degraded infiltration. The aim of this work was to evaluate the respective influences of sediment deposition and biofilm biomass on the deterioration of hydraulic performances in two infiltration basins used for groundwater recharge. Samples were collected by coring in the two basins. Grain size distribution (with and without organic matter), bacterial and algal biomasses, and microbial activity were measured at three depths from the soil surface (0–1 cm, 2–3 cm and 10–14 cm). In parallel, in situ single-ring infiltration tests were performed before and after removal of the top layer (0–1 cm). The results showed considerably reduced permeability due to clogging of the top sedimentary layer in the two basins. The highest reduction of permeability was measured in the basin colonized by the largest algal biomass. The proportions of fine mineral particles (<63 μm) were comparable in the two basins and could not explain their differences in saturated hydraulic conductivities. In addition, the relationships between biological and hydraulic parameters highlighted a threshold effect of algal biomass on the structure of the pore network, possibly explaining the decrease in infiltration. This original link between hydraulic and microbial characteristics suggests that algal biofilm growth had a major impact on the hydraulic performance of the infiltration basins. Copyright © 2013 John Wiley & Sons, Ltd.