Farm ponds must be regularly sampled for Escherichia coli (E. coli) concentrations to evaluate the health risks of using pond water for irrigation. However, no guidance is available regarding sampling locations and/or irrigation pump placement. We hypothesized that there exists spatial and/or temporal patterns of E. coli concentrations across ponds. To test this hypothesis, we sampled two irrigation ponds in Maryland biweekly during the summers of 2016 and 2017. Results from data analysis of mean relative differences and Spearman correlation coefficients are presented. Empirical orthogonal functions indicated spatial patterns of Log E. coli concentrations were temporally maintained. More sample variance existed over time in the pond interiors versus near shore locations. Furthermore, larger patterns of sample variance existed within the spatial analysis variance versus the temporal analysis variance over both ponds for this study. Therefore, the spatio-temporal E. coli variance may have significant impacts on sampling and pump intake locations.