Pilot-scale direct filtration challenge experiments were conducted to determine the impact of chemical pretreatment and filter design on the removal of Cryptosporidium surrogates dosed into the filter influent water at low temperatures (Average 0.5 °C). Copolymers-modified microspheres were identified as representative Cryptosporidium oocysts surrogates based on our previous findings and were used to evaluate the oocysts filtration removal at this pilot-scale study. The operational parameters examined included coagulant type (aluminum sulfate (alum) versus polyaluminium chloride (PACl)), filter aid polymer type (polyamine Magnafloc® LT-7981 versus poly(Dimethyl Diallyl Ammonium Chloride) (polyDADMAC) Magnafloc® LT-7995) and dose (0.5 versus 2.0 mg/L), and filter configuration (regular versus deep bed filters). The study found that higher Cryptosporidium surrogate removal was associated with higher polymer dose (2 mg/L) of polyDADMAC polymer and the deep bed filter configuration. The difference in surrogate removal between PACl and alum was no significant at cold temperature conditions tested. The deep bed filters were associated with higher surrogate removal, while exhibiting lower rates of flow reduction and longer filter run time. This work emphasizes the importance of optimizing chemical pretreatment and filter configuration for removing surrogates of Cryptosporidium oocysts in cold-water conditions in granular media water filtration processes. This pilot-scale study also demonstrated the exceed 2.5-log removal of Cryptosporidium surrogates (required from Guideline for Canadian Drinking Water Quality) can be achieved in the direct filtration during Edmonton cold-water condition when the pretreatment processes are optimized using 0.454 mg/L of alum as Al with addition of 0.5 mg/L poly DADMAC.