The standard procedure outlined by the United States Environmental Protection Agency (US EPA) in Method 1623 for analyzing Giardia lamblia cysts and Cryptosporidium parvum oocysts in water samples consists of filtration, elution, centrifugal concentration, immunomagnetic separation (IMS), and immunofluorescence assay (IFA) followed by microscopic examination. In this study, the extent of (oo)cyst loss in each step of this procedure was evaluated by comparing recovery yields in segmented analyses: (i) IMS + IFA, (ii) concentration + IMS + IFA, and (iii) filtration/elution + concentration + IMS + IFA. The complete (oo)cyst recovery by the full procedure was $52{sim}57%$. The (oo) cyst loss in the IMS step was only $0{sim}6%$, implying that IMS is a fairly reliable method for (oo)cyst purification. Centrifugal concentration of the eluted sample and pellet collection before IMS resulted in a loss of $8{sim}14%$ of the (oo)cysts. The largest (oo)cyst loss occurred in the elution step, with $68{sim}71%$ of the total loss. The permeated loss of (oo)cysts was negligible during filtration of the water sample with a $1.0-{mu}m$ pore polyethersulfone (PES) capsule. These results demonstrated that the largest fraction of (oo)cyst loss in this procedure occurred due to poor elution from the filter matrix. Improvements in the elution methodology are therefore required to enhance the overall recovery yield and the reliability of the detection of these parasitic protozoa.