Pilot-scale column experiments were conducted in this study using natural soil and river water from Ohio river to assess the removal of microbes of size ranging over 2 orders of magnitude, i.e., viruses (0.025-0.065 microm), bacteria (1-2 microm), and Cryptosporidium parvum oocysts (4-7 microm) under conditions representing normal operation and flood scour events. Among these different organisms, the bacterial indicators were transported over the longest distances and highest concentrations; whereas much greater retention was observed for smaller (i.e., viral indicators) and larger (i.e., Cryptosporidium parvum oocysts) microbes. These results are in qualitative agreement with colloid filtration theory (CFT) which predicts the least removal for micrometer size colloids, suggesting that the respective sizes of the organisms was a dominant control on their transport despite expected differences in their surface characteristics. Increased fluid velocity coupled with decreased ionic strength (representative of major flood events) decreased colloid retention, also in qualitative agreement with CFT. The retention of organisms occurred disproportionately near the source relative to the log-linear expectations of CFT, and this was true both in the presence and absence of a colmation zone, suggesting that microbial removal by the RBF system is not necessarily vulnerable to flood scour of the colmation zone.