Cyanobacteria and their toxins can have multiple effects on agricultural productivity and water bodies. Cyanotoxins can be transported to nearby crops and fields during irrigation and may pose a risk to animal health through water sources. Spatial and temporal variations in cyanotoxin concentrations have been reported for large freshwater sources such as lakes and reservoirs, but there are fewer studies on smaller agricultural surface water bodies. To determine whether spatiotemporal patterns of the cyanotoxin microcystin occurred in agricultural waters used for crop irrigation and livestock watering, three agricultural ponds on working farms in Georgia, USA, were sampled monthly within a fixed spatial grid over a 17-month period. Microcystin concentrations, which ranged between 0.04 and 743.75 ppb, were determined using microcystin–ADDA ELISA kits. Temporal stability was assessed using mean relative differences between microcystin concentrations at each location and averaged concentrations across ponds on each sampling date. There were locations or zones in all three ponds that were consistently higher or lower than the average daily microcystin concentrations throughout the year, with the highest microcystin concentrations occurring in winter. Additionally, microcystin patterns were strongly correlated with the patterns of chlorophyll, phycocyanin, and turbidity. The results of this work showed that consistent spatiotemporal patterns in cyanotoxins can occur in produce irrigation and livestock watering ponds, and this should be accounted for when developing agricultural water monitoring programs.