The quality of irrigation water drawn from surface water sources can vary greatly. This is particularly true for waters that are subject to intermittent contamination events such as runoff or direct entry of livestock upstream of use. Such pollution in irrigation systems increases the risk of food crop contamination. A single sample does not adequately characterize the risk potential present in large irrigation systems often utilized in the Southwestern US. This project aimed to define optimal monitoring strategies for irrigation water quality and develop guidelines for the irrigation of food crops. Following the analysis of 1,367 samples for Escherichia coli and physical and environmental parameters, the following key irrigation water collection approaches are suggested: 1) Explore up to 600m upstream to ensure no major contamination or outfalls exists; 2) Sample before noon; 3) Collect samples at any point across the canal where safe access is available; 4) Collect samples at the surface of the water; and 5) Composite five samples and perform a single E. coli assay. These recommendations consider the entirety of our data as well as sampling costs, personnel effort, and scientific knowledge of water quality characterization in the Southwest region. These guidelines will better characterize risks from microbial pathogen contamination in irrigation waters and aid in risk reduction practices for agricultural water.