The objective of this study is to compare the removal of Taenia eggs to the removal of Ascaris eggs in a wastewater stabilization pond system consisting of three ponds in series, where the hydraulic residence time distribution has been characterized via a tracer study supported by computational fluid dynamics modeling. Despite a theoretical hydraulic retention time of 30 days, the peak dye concentration was measured in the effluent of the first pond after only 26 hours. The smaller-sized Taenia eggs were detected in higher concentrations than Ascaris eggs in the raw wastewater. Ascaris eggs were not detected in the pond system effluent, but 45 Taenia eggs/L were detected in the system effluent. If some of these eggs were of the species Taenia solium, and if the treated wastewater were used for the irrigation of crops for human consumption, farmers and consumers could potentially be at risk for neurocysticercosis. Thus, limits for Taenia eggs in irrigation water should be established, and precautions should be taken in regions where pig taeniasis is endemic. The results of this study indicate that the theoretical hydraulic retention time (volume/flow) of a pond is not always a good surrogate for helminth egg removal.