Wastewater treatment plants (WWTPs) form an industry whose main goal is to reduce water’s pollutant products, which are harmful to the environment at high concentrations. In addition, regulations are applied by administrations to limit pollutant concentrations in effluent. In this context, control strategies have been adopted by WWTPs to avoid violating these limits; however, some violations still occur. For that reason, this work proposes the deployment of an artificial neural network (ANN)-based soft sensor in which a Long-Short Term Memory (LSTM) network is used to generate predictions of nitrogen-derived components, specifically ammonium ( $S_{NH}$ ) and total nitrogen ( $S_{Ntot}$ ). $S_{Ntot}$ is a limiting nutrient and can therefore cause eutrophication, while nitrogen in the $S_{NH}$ form is toxic to aquatic life. These parameters are used by control strategies to allow actions to be taken in advance and only when violations are predicted. Since predictions complement control strategies, the evaluation of the ANN-based soft sensor was carried out using the Benchmark Simulation Model N.2. (BSM2) and three different control strategies (from low to high control complexity). Results show that our proposed method is able to predict nitrogen-derived products with good accuracy: the probability of detecting violations of BSM2’s limits is 86–94%. Moreover, the prediction accuracy can be improved by calibrating the soft sensor; for example, perfect prediction of all future violations can be achieved at the expense of increasing the false positive rate.