Processing source separated urine with clinoptilolite is one effective method for nutrient recovery from urine where ion exchange/adsorption is the predominating process. Although this method can be applied in either batch or continuous mode, almost all work in the literature has been focused on the batch mode. The aim of this work was to determine and to compare surface capacities and operation times for both of these two modes to identify the more effective one for nutrient recovery under similar conditions. Using initial ammonium loadings between 10-40 mg ammonium/g clinoptilolite for the batch mode and empty bed contact times between 30-120 min for the continuous mode, it was observed that higher surface capacities and lower operation times were achieved in the continuous mode while higher efficiencies and lower residual concentrations were observed for the batch mode. From the stand point of surface capacities and operation times, continuous mode seems preferable over batch operation for nutrient recovery from human urine with clinoptilolite through ion exchange/adsorption.