In order to reduce aquaculture risks and optimize the operation of water quality management in prawn engineering culture ponds, this paper proposes a novel water temperature forecasting model based on empirical mode decomposition (EMD) and back-propagation neural network (BPNN). First, the original water temperature datasets are decomposed into a collection of intrinsic mode functions (IMFs) and a residue by EMD yields relatively stationary sub-series that can be readily modeled by BPNN. Second, both IMF components and residue is applied to establish the corresponding BPNN models. Then, each sub-series is predicted using the corresponding BPNN. Finally, the prediction values of the original water temperature datasets are calculated by the sum of the forecasting values of every sub-series. The proposed hybrid model was applied to predict water temperature in prawn culture ponds. Compared with traditional models, the simulation results of the hybrid EMD–BPNN model demonstrate that de-noising and capturing non-stationary characteristics of water temperature signals after EMD comprise a very powerful and reliable method for predicting water temperature in intensive aquaculture accurately and quickly.