Assessment of wastewater effluent quality in terms of physicochemical and microbial parameters is a difficult task; therefore, an online method which combines the variables and represents a final value as the quality index could be used as a useful management tool for decision makers. However, conventional measurement methods often have limitations, such as time-consuming processes and high associated costs, which hinder efficient and practical monitoring. Therefore, this study presents an approach that underscores the importance of using both short- and long-term memory networks (LSTM) to enhance monitoring capabilities within wastewater treatment plants (WWTPs). The use of LSTM networks for soft sensor design is presented as a promising solution for accurate variable estimation to quantify effluent quality using the total chemical oxygen demand (TCOD) quality index. For the realization of this work, we first generated a dataset that describes the behavior of the activated sludge system in discrete time. Then, we developed a deep LSTM network structure as a basis for formulating the LSTM-based soft sensor model. The results demonstrate that this structure produces high-precision predictions for the concentrations of soluble X1 and solid X2 substrates in the wastewater treatment system. After hyperparameter optimization, the predictive capacity of the proposed model is optimized, with average values of performance metrics, mean square error (MSE), coefficient of determination (R2), and mean absolute percentage error (MAPE), of 23.38, 0.97, and 1.31 for X1, and 9.74, 0.93, and 1.89 for X2, respectively. According to the results, the proposed LSTM-based soft sensor can be a valuable tool for determining effluent quality index in wastewater treatment systems.