Experimental studies of nutrient removal in a discontinuous downflow two-media filter on a pilot plant scale are described and compared with previously reported results from a continuous upflow filter (DynaSand) studied at full scale. Under controlled conditions both filters show low effluent values of total nitrogen and phosphorus. Removal mechanisms were more complex in the discontinuous downflow filter owing to the use of two media, deposition of sludge on the filter surface, and changes of the biological activity over time after backwashing. The discontinuous downflow filter was much influenced by the formation of nitrogen gas bubbles clogging the filter, while the influence of nitrogen gas formation in the DynaSand filter was minor. Multivariate methods were used to evaluate factors influencing nitrate and phosphate removal and the time passing before the filter became clogged.