Filter backwash water (FBW) is a prominent residue from water treatment plants (WTPs) that is often disposed into water bodies or recycled within the WTP without due disinfection. FBW usually contains particles within a size range that includes pathogenic protozoa, as the infective forms of Giardia and Cryptosporidium, parasites responsible for waterborne diseases outbreaks. Quantifying (oo)cysts is essential for addressing this matter, as it might assist research on giardiasis and cryptosporidiosis epidemiology, as well as shed light onto disinfection technologies for FBW. However, (oo)cyst recovery from FBW and other complex matrices still lacks a standard protocol and entails specialized professionals and expensive material. Seeking to provide insight in a reduced-cost recovery method, this study analysed the recovery efficiency (RE) obtained by acid flocculation with ferric sulphate, a common coagulant, on bench-scale simulated FBW. Steps included concentration by flocculation, centrifugation, and quantification by immunofluorescence. Although recovery was sufficient for Cryptosporidium parvum (40.59%), Method 1623.1 recommendations were not reached for Giardia muris (1.76%). Coefficients of variation obtained for both organisms were not satisfactory, highlighting the variability to which environmental matrices are subjected and why defining a methodology for (oo)cyst recovery in WTP residues is important.