This study explores the loss or degradation of the ecosystem and its service function in the Liaohe estuary coastal zone due to the deterioration of water quality. A prediction system based on support vector machine (SVM)-particle swarm optimization (PSO) (SVM-PSO) algorithm is proposed under the background of deep learning. SVM-PSO algorithm is employed to analyze the pollution status of the Liaohe estuary, so is the difference in water pollution of different sea consuming types. Based on the analysis results for causes of pollution, the control countermeasures of water pollution in Liaohe estuary are put forward. The results suggest that the water pollution index prediction model based on SVM-PSO algorithm shows the maximum error of 2.41%, the average error of 1.24% in predicting the samples, the root mean square error (RMSE) of 5.36 × 10−4, and the square of correlation coefficient of 0.91. Therefore, the prediction system in this study is feasible. At present, the water pollution status of Liaohe estuary is of moderate and severe levels of eutrophication, and the water pollution status basically remains at the level of mild pollution. The general trend is from phosphorus moderate restricted eutrophication to phosphorus restricted potential eutrophication. To sum up, the SVM-PSO algorithm shows good sewage prediction ability, which can be applied and promoted in water pollution control and has reliable reference significance.