Three estuarine macroalgae (Ulva rotundata, Enteromorpha intestinalis, Gracilaria gracilis) of economic potential were cultivated in the laboratory to assess their biofiltering capacities for ammonium in waste effluents from a sea bass (Dicentrarchus labrax) cultivation tank. The study was developed to investigate the functioning of N nutrition of the three species. At low water flow (< 2 volumes d(-1)) the three species stripped efficiently the ammonium dissolved in the waste water from the fish tank, with a minimum biofiltering efficiency estimate of 61% in unstarved cultures of G. gracilis at a water flow of 2 volumes d(-1). Maximum velocity for ammonium uptake (89.0 mu mol NH4+ g(-1) dry wt h(-1)) was found in U. rotundata, whereas G. gracilis showed the highest affinity for this nutrient. The net ammonium uptake rate was significantly affected by the water flow, being greatest at the highest flow assayed (2 volumes d(-1)). Variations of tissue N and C: N ratios during a flow-through experiment suggested that N was not limiting macroalgal growth. However, when ammonium was supplied at a flow rate of 0.5 volumes d(-1), specially in a three-stage design, the marked reduction in tissue N and the biomass C: N: P ratios suggested a more general nutrient deficiency. A significant correlation was found between growth rates and the N biomass gained in the cultures. The three-stage design under low water flow (0.5 volumes d(-1)) showed that the highest ammonium uptake rates (up to 80.9 mumol NH4+ g(-1) dry wt d(-1) in U. rotundata) were found in the first stage, with decreasing rates in the following ones. As a result, low increments or even losses of total N biomass in these stages were found, suggesting that ammonium was excreted from the algae. We conclude that these species present a potential ability to biofilter the ammonium dissolved in waste water from a D. labrax cultivation tank, suggesting that scaling up the biofiltration designs, future practises using these macroalgae may be implemented in the local fish farms, resulting in both environmental and economical advantages.