The design of trickling filters used on commercial eel farms differs considerably with respect to dimensions, hydraulic and substrate loads and filter medium applied. In this paper, a model, developed for ammonium removal in a pilot-scale trickling filter, has been validated for a range of full-scale trickling filters, incorporating the above mentioned aspects. The performance of trickling filters was assessed at 14 commercial eel farms in The Netherlands. Analysis of the data obtained has shown that the model sufficiently explains and predicts the ammonium removal rate of a wide range of commercial trickling filters. The model is used to optimise performance of existing biofilters in terms of ammonium levels achieved and pumping costs. Observations have also been made on nitrite in recirculation systems. Concentrations of nitrite and the ratio between nitrite and ammonium vary widely in and between systems. The nitrite oxidation capacity in biofilms seems to be variable and sensitive to environmental disturbances.