This study evaluated the effects of isonitrogenous feeding (60 g dietary protein per kilogram of body weight per day) using experimental feeds with 25%, 30%, 35% and 40% protein on the nitrogen budget, ammonia efflux rate, growth and survival of juvenile Litopenaeus vannamei raised in a low-salinity (4 g L−1) zero-water exchange culture system for 4 weeks. No significant differences in weight gain or instantaneous growth rate were observed between the dietary treatments with 35% and 40% protein after 3 weeks of study, or between treatments with 25% and 30% protein after 4 weeks of study. High mortality rates were observed for the 35% and 40% protein treatments, probably associated with high nitrite levels (4.80 and 7.36 mg NO2-NL−1 respectively) in water. Among the various dietary treatments, 39–46.3% of feed nitrogen was converted to shrimp biomass, 32.8–38.0% and 14.4–39.9% remained within the system as organic and inorganic nitrogen, respectively, and 32.5–39.3% was unaccounted for. The results of the present study showed high nitrogen utilization efficiencies. However, as the nitrogen loading of the zero-water exchange system increased, so did the nitrogen excretion of shrimp, causing a deteriorated general condition of the shrimp, demonstrated by the low ammonia efflux rates recorded at the end of the trial. This study confirms that low-salinity closed systems are particularly susceptible to nitrogen loading. Thus, in these culture systems, low-protein feeds may perform better as they provide more carbon for heterotrophic bacteria and less nitrogen to be degraded and transformed into nitrogenous wastes.