Monitoring the removal of Cryptosporidium oocysts in water treatment plants is a challenge, particularly in developing countries, and the use of surrogates has proven necessary. Two surrogates already investigated and recognized by the scientific community are aerobic spore-forming bacteria (ASFB) and fluorescent polystyrene microspheres (ME). In this context, this study evaluates and compares the performance of upflow direct filtration and downflow direct filtration, with emphasis on the removal of ASFB and ME as a surrogate of Cryptosporidium oocyst removal. Pilot filtration experiments were carried out with low turbidity Paranoá Lake water (average—3.7 NTU) with ASFB varying from 7 × 102 to 5.5 × 103 CFU/100 mL. In some experiments, water was spiked with microspheres, aiming for 105 ME/L. Two operational conditions were evaluated: (1) filters operating with the same filtration rate (5 m/h); (2) filters operating with the same flow rate of 59.41 L/h. In general, the downflow filter presented a slightly higher removal efficiency than the upflow filter but the differences were not considered statistically significant in most cases. The removal efficiency of microspheres (3 to 5 log) was higher than that of ASFB (1.2 to 4 log) in both filters, corroborating that the removal of ASFB is a conservative surrogate of the removal of Cryptosporidium.