Cryptosporidium parvum is a pathogen causing gastrointestinal infections, occasionally leading to death in immunocompromised individuals. It can contaminate surface water and groundwater, and consequently drinking water supplies, through agricultural activities such as cattle and dairy farming or the spreading of manure as fertilizer. The importance of removing C. parvum by filtration is of great interest because of its long-term persistence in water as oocysts and its resistance to chemical disinfection owing to its thick cell wall. This is relevant for both subsurface filtration and engineered filtration processes. Therefore, it is necessary to evaluate its removal efficiency in subsurface media and during the filtration stage of drinking water treatment. This study aimed to select an appropriate surrogate for C. parvum oocysts that exhibits similar attenuation and transport behaviour through porous media, is cost-effective, and poses no harm to humans or the environment, enabling its application in engineered installations and field studies. Bacillus subtilis is commonly used as a conservative surrogate for C. parvum for subsurface transport studies, and aerobic spores have been included by the U.S. Environmental Protection Agency as an indicator for C. parvum in groundwater under the direct influence (GWUDI) of surface water. While B. subtilis may be a cost-effective option, its smaller size (nearly 6 times smaller in diameter), different shape (rod-shaped vs. spherical), and distinct surface characteristics present limitations. This study evaluated the attenuation and transport of B. subtilis spores, oocyst-sized unmodified (yellow-green and yellow-orange) and glycoprotein-coated microspheres, along with UV inactivated C. parvum in columns packed with silica sand. The objective was to determine the significance of size, surface charge, and macromolecules on the cell wall surface, on the reduction of the oocysts. Glycoprotein-coated microspheres, exhibiting similar physicochemical properties (including macromolecules) to oocysts, were found to be the most effective surrogate. The study results highlight the importance of selecting appropriate surrogates for accurate evaluation of the transport of C. parvum in the subsurface and its removal in water treatment through sand filtration.