Excretion of nutrients by zooplankton is a complex process crucial for the functioning of aquatic ecosystems. Most of the available literature data concern excretion in freshwater or marine ecosystems, but little is known about the nutrients regeneration in brackish water bodies, and the described research results are often inconclusive. Therefore, the aim of this study was to investigate the intravital release of nitrogen and phosphorous in brackish water bodies and to analyze the effect of salinity levels on the process of excretion. Studies on excretion were based on laboratory experiments. In 2010, the rate of intravital release of nutrients by zooplankton sampled from the natural environment of the Vistula Lagoon and Lake Łebsko was analyzed in order to estimate the rate of excretion of nitrogen and phosphorus depending on the salinity level. A similar experiment was also carried out on monocultures of Brachionus calyciflorus. Results from studies on natural populations revealed variable rates of nutrients excretion for different levels of salinity. This correlation, however, was not statistically significant. Experiments on B. calyciflorus monocultures showed a significant (p < 0.05) linear correlation between salinity and excretion. The study demonstrated that higher concentrations of salts dissolved in water accelerate the rate of nutrients regeneration by zooplankton. The investigated process is determined by many factors, and for the reliable estimation of the excretion rate a multivariate analysis should be performed.