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EPA Method 1623 for the recovery, detection and enumeration of Cryptosporidium and Giardia from water represents significant advances over earlier methods. However, protozoa recovery efficiency remains variable, depending upon water matrices and other factors, yielding potentially misleading results. This problem is exacerbated as modified versions of the method are increasingly applied to non-routine matrices, in part due to the focus on reclaimed water. To assess the effect of a particular matrix on recovery efficiency of protozoa, Method 1623 requires that a matrix spike (MS) sample be collected along with the field sample within every 20 samples from a particular source. While better than no recovery data, the validity of this approach for assessing matrix effect within a given sample set and across a set of 20 samples, depends upon: the homogeneity of the field sample and the MS sample in terms of indigenous protozoa concentration and potential interferences, within the given sampling event; and, the temporal consistency of the water matrix over the 19 sample interval between successive MS samples. Includes extended abstract only.