Continuous effluent quality prediction in wastewater treatment processes is crucial to proactively reduce the risks to the environment and human health. However, wastewater treatment is an extremely complex process controlled by several uncertain, interdependent, and sometimes poorly characterized physico-chemical-biological process parameters. In addition, there are substantial spatiotemporal variations, uncertainties, and high non-linear interactions among the water quality parameters and process variables involved in the treatment process. Such complexities hinder efficient monitoring, operation, and management of wastewater treatment plants under normal and abnormal conditions. Typical mathematical and statistical tools most often fail to capture such complex interrelationships, and therefore data-driven techniques offer an attractive solution to effectively quantify the performance of wastewater treatment plants. Although several previous studies focused on applying regression-based data-driven models (e.g., artificial neural network) to predict some wastewater treatment effluent parameters, most of these studies employed a limited number of input variables to predict only one or two parameters characterizing the effluent quality (e.g., chemical oxygen demand (COD) and/or suspended solids (SS)). Harnessing the power of Artificial Intelligence (AI), the current study proposes multi-gene genetic programming (MGGP)-based models, using a dataset obtained from an operational wastewater treatment plant, deploying membrane aerated biofilm reactor, to predict the filtrated COD, ammonia (NH4), and SS concentrations along with the carbon-to-nitrogen ratio (C/N) within the effluent. Input features included a set of process variables characterizing the influent quality (e.g., filtered COD, NH4, and SS concentrations), water physics and chemistry parameters (e.g., temperature and pH), and operation conditions (e.g., applied air pressure). The developed MGGP-based models accurately reproduced the observations of the four output variables with correlation coefficient values that ranged between 0.98 and 0.99 during training and between 0.96 and 0.99 during testing, reflecting the power of the developed models in predicting the quality of the effluent from the treatment system. Interpretability analyses were subsequently deployed to confirm the intuitive understanding of input-output interrelations and to identify the governing parameters of the treatment process. The developed MGGP-based models can facilitate the AI-driven monitoring and management of wastewater treatment plants through devising optimal rapid operation and control schemes and assisting the plants’ operators in maintaining proper performance of the plants under various normal and disruptive operational conditions.