Microbial contamination in surface waters has become a worldwide cause for concern. As efforts are made to reduce this contamination, monitoring is integral to documenting and evaluating water quality improvements. Autosamplers are beneficial in such monitoring efforts, as large data sets can be generated with minimized effort. The extent to which autosamplers can be utilized for microbial monitoring is largely unknown due to concerns over contamination. Strict sterilization regimes for components contacting the water being sampled are difficult, and sometimes logistically implausible, when utilizing autosamplers. Field experimentation showed contamination of fecal coliform in autosamplers to be more of a concern than that of Escherichia coli. Further study in a controlled laboratory environment suggested that tubing configuration has a significant effect on residual E. coli concentrations in sampler tubing. The amount of time that passed since the last sample was collected from a given sampler (antecedent dry weather period - DWP) tubing was also a significant factor. At a DWP of 7 days, little to no contamination was found. Thus, simple protocols such as providing positive drainage of tubing between sample events and programming samplers to include rinses will reduce concerns of contamination in autosamplers.