Land application of dairy soiled water (DSW) is expensive relative to its nutrient replacement value. The use of aerobic filters is an effective alternative method of treatment and potentially allows the final effluent to be reused on the farm. Knowledge gaps exist concerning the optimal design and operation of filters for the treatment of DSW. To address this, 18 laboratory-scale filters, with depths of either 0.6 m or 1 m, were intermittently loaded with DSW over periods of up to 220 days to evaluate the impacts of depth (0.6 m versus 1 m), organic loading rates (OLRs) (50 versus 155 g COD m-2d-1), and media type (woodchip versus sand) on organic, nutrient and suspended solids (SS) removals. The study found that media depth was important in contaminant removal in woodchip filters. Reductions of 78% chemical oxygen demand (COD), 95% SS, 85% total nitrogen (TN), 82% ammonium-nitrogen (NH4-N), 50% total phosphorus (TP), and 54% dissolved reactive phosphorus (DRP) were measured in 1 m deep woodchip filters, which was greater than the reductions in 0.6 m deep woodchip filters. Woodchip filters also performed optimally when loaded at a high OLR (155 g COD m-2 d-1), although the removal mechanism was primarily physical (i.e. straining) as opposed to biological. When operated at the same OLR and when of the same depth, the sand filters had better COD removals (96%) than woodchip (74%), but there was no significant difference between them in the removal of SS and NH4-N. However, the likelihood of clogging makes sand filters less desirable than woodchip filters. Using the optimal designs of both configurations, the filter area required per cow for a woodchip filter is more than four times less than for a sand filter. Therefore, this study found that woodchip filters are more economically and environmentally effective in the treatment of DSW than sand filters, and optimal performance may be achieved using woodchip filters with a depth of at least 1 m, operated at an OLR of 155 g COD m-2 d-1.