With the goal of improving water quality control, in this study we combined CE-LIF for the analysis of Escherichia coli lysates under discontinuous conditions. Prior to injecting a large-volume protein sample, a plug of 0.2% w/v SDS was injected into the capillary filled with 2.0 M Tris-borate (TB) solution (pH 10.3). During the courses of the process stacking, proteins migrated against the electroosmotic flow (EOF) and entered a 1.7% w/v poly(ethylene oxide) solution that has been prepared in 200 mM TB (pH 9.0). The stacked proteins were then separated through sieving and then detected at the cathodic end. The use of TB solutions containing 0.01% w/v poly(ethylene oxide) was essential for the preparation of the protein samples and E. coli lysates to minimize the extent of protein adsorption on the capillary wall. Under the optimized CE-LIF conditions, we detected beta-Galactosidase with and without concentration at levels as low as 0.23 and 7.52 nM, respectively. Our approach allowed the detection of 3 x 10(2) E. coli cells based on the characteristic peaks of its lysates; in addition, we could detect the presence of 20 E. coli cells in a 50 mL sample of pond water within 24 h. In terms of the analyte migration time, the relative standard deviation of this CE-LIF method was less than 1.3%. We also extended the practicality of this technique by applying it to the separation of mixtures of E. coli, Enterobacter aerogenes, and Salmonella enterica.