Due to the heterogeneity of recycled paper materials and the production conditions, pollutants in papermaking wastewater fluctuate sharply over time. Quality control of the papermaking wastewater treatment process (PWTP) is challenging and costly. As regulations are also growing about the environmental effects of the PWTP on greenhouse gas (GHG) emission, energy consumption, etc., the PWTP formulates a complex multiobjective optimization problem. This research established a multiagent deep reinforcement learning framework to simultaneously optimize process cost, energy consumption, and GHG emission in the PWTP, subjected to the effluent quality, to realize economic, energy, and environmental (3E) goals. The biological treatment process of wastewater in paper mills was simulated using benchmark simulation model no. 1 (BSM1). The data generated based on the BSM manual was utilized for model training, and real data acquired from a local papermaking factory was used to estimate the model performance. The results show that the proposed method outperforms conventional techniques in identifying the best control strategies for multiple targets.