The limited efficacy of disinfectants, other than ultraviolet irradiation and ozonation, as a barrier against Cryptosporidium parvum in drinking water treatment has underscored the increased importance of oocyst removal by filtration. Currently, no reliable surrogates have been identified for C. parvum removal by filtration. As a result, evaluations of the Cryptosporidium removal by treatment operations have been performed using oocysts. It has typically been assumed that chemically inactivated oocysts are suitable surrogates for viable oocysts. Measurements of electrophoretic mobility, however, have shown that chemical inactivation changes the surface charge of Cryptosporidium oocysts. The present bench-scale research indicated that formalin-inactivated oocysts are reliable surrogates for viable oocysts during both stable filter operation and periods where filtration processes are challenged, such as coagulation failure. This finding is important because of the practical difficulties associated with using viable oocysts in filtration investigations. Poor coagulation conditions severely compromised removal of viable and inactivated oocysts by dual- and tri-media filters compared to stable operating conditions and filter ripening, emphasizing the importance of optimized chemical pre-treatment (coagulation) for the successful removal of oocysts during filtration. The treatment optimization experiments also indicated that tri-media filters offered only marginally higher oocyst removals than dual-media filters.