In this study, we used clinoptilolite and mordenite, which are the most widely used and researched natural zeolites, to establish 72-hour dynamic adsorption curves of ammonium at different total ammonia nitrogen (TAN) concentrations, salinity levels and pH values. The results showed that mordenite is more efficient for ammonium removal than clinoptilolite. At equal TAN concentrations, it took five times as much clinoptilolite as mordenite to achieve similar amounts of ammonium adsorption. The salinity level was a major interference factor in zeolite ammonium adsorption, with a salinity level of only 5 psu reducing the adsorption capability markedly. Specifically, the adsorption capabilities of clinoptilolite and mordenite were 30 and 20% of their respective capabilities in fresh water, with clinoptilolite performing better in the face of interference due to salinity. In addition, there were no significant differences between in the adsorption capacities of either clinoptilolite or mordenite as the salinity levels were increased from 5–30 psu (p > 0.05). The range of pH was 4–10 in this study, and the best performances of clinoptilolite and mordenite were at pH 6 and 5–7, respectively. According to these results and the costs of the zeolites, mordenite is a better ammonium adsorbent than clinoptilolite. We also established linear regressions for reduced TAN and provided a basis for using mordenite to treat TAN at 2–10 ppm, based on the safe concentrations of ammonia nitrogen for fresh water aquaculture species.