Herbicides applied to container plants in nurseries are transported in runoff water to on- and off-site ponds and retention basins. This study was conducted to determine biotic and abiotic effects on isoxaben dissipation in model flow-through retention basins to maximize aqueous isoxaben degradation. Field studies were conducted in 1999 and 2000 to evaluate the effects of gravel and pine bark amendments and water retention times on isoxaben persistence in holding basins. In 1999, total isoxaben discharge into flow-through gravel-filled basins was greater than isoxaben losses from gravel and nongravel basins in which water was retained. Photodegradation appeared to be greater in basins without gravel, indicating that gravel protected isoxaben from photolysis. Further studies determined the effect of water retention time and the presence of aged pine bark amendment on isoxaben discharge from basins. Isoxaben discharge level was reduced when water retention time was increased from 3 to 5 d. In the 3-d retention time treatment, added pine bark reduced peak isoxaben discharge by 45% and total isoxaben by 53% at 14 d after treatment. In treatments containing pine bark within the retention basins, isoxaben was released over a longer period of time. No differences were observed in 5-d water retention time treatments with and without pine bark. Analysis of gravel from isoxaben-treated retention basins indicated the presence of several genera of bacteria including Pseudomonas, Arthrobacter, and Cellulomonas. Some isolates of Pseudomonas, Rahnella, Methobacterium, and Paenibacillus from the basins grew on M9 medium with isoxaben as the sole carbon and energy source, indicating their ability to metabolize isoxaben. Results indicate that retention basins are helpful in reducing isoxaben levels before release or reuse of runoff water from a container nursery, and that retention time of runoff water in basins is the most important factor in reducing isoxaben discharge.