There has been a resurgence of interest, technological advancement, and implementation of biologically active slow sand filtration technologies for small-scale potable water treatment in North America. Modelling the fate and transport of pathogenic microorganisms is vital to assess technological safety and for licensing, permitting and regulatory validation. The efficacy of a modified slow sand (MSS) filter treatment technology to produce drinking water and remove Cryptosporidium oocyst-sized particles was tested using a rural raw water source seeded with 4–4.9 μm (mean 4.5 μm) microsphere surrogates. The turbidity, temperature, pH and total organic carbon content of raw water were 1.46 ± 0.010 nephelometric turbidity unit (NTU), 3.40 ± 0.30 °C, 8.05 ± 0.16 and 22.7 ± 0.64 mg/L, respectively, and those of the MSS filter effluent with biologically active carbon filter influent were 0.47 ± 0.0 NTU, 3.36 ± 0.42 °C, 7.90 ± 0.27 and 22.6 ± 0.65 mg/L. The decimal elimination capacity of the MSS and biologically active carbon filters for the microspheres were at least 2 and 1 log at 95% confidence, respectively. These systems are capable of removing oocyst-sized particles under extreme conditions, providing safe, effective and economical treatment solutions for small-scale municipal drinking water.