Although the management and planning of water resources are extremely significant to human development, the complexity of implementation is unimaginable. To achieve this, the high-precision water consumption prediction is actually the key component of urban water optimization management system. Water consumption is usually affected by many factors, such as weather, economy, and water prices. If these impact factors are directly combined to predict water consumption, the weight of each perspective on the water consumption will be ignored, which will be greatly detrimental to the prediction accuracy. Therefore, this paper proposes a deep neural network-based complex system for urban water management. The essence of it is to formulate a water consumption prediction model with the aid of principal component analysis and the integrated deep neural network, which is abbreviated as UWM-Id. The PCA classifies the factors affecting water consumption in the original data into three categories according to their correlation and inputs them into the neural network model. The results in the previous step are assigned weights and integrated into the form of fully connected layer. Finally, analyzing the sensitivity of the proposed UWM-Id and comparing its performance with a series of commonly used baseline methods for data mining, a large number of experiments have proved that UWM-Id has good performance and can be used for urban water management system.