Internet of Things (IoT) technology provides the necessary foundation and support for smart city water management. To address the challenge of river pollution prevention and flood control requirements in the urban river system, this article proposes a data-driven model to carry out the optimal operation scheduling of water diversion and drainage pumping stations in the presence of the complex hydrometeorological constraints. The proposed solution in the model predictive control (MPC) framework first adopts the long short-term memory (LSTM) network through supervised learning from IoT data to simulate and predict the river flow dynamics and the water quality. Consequently, the optimal scheduling of controllable pumping stations to minimize the operational cost (e.g., the flocculant consumption) can be formulated as a stochastic optimization problem, while meeting the river flood control and water quality constraints. The particle swarm optimization (PSO) algorithm is further used to solve the above unit commitment (UC) optimization problem and obtain the optimal operational schedules of the water pumping units (e.g., startup time and working periods). The performance of the proposed optimal water pumping scheduling solution is evaluated through a field case study of the urban river diversion system and the numerical results clearly confirm its effectiveness and improved economic performance compared to the existing benchmark solution.