Factor analysis was conducted to explain the characteristics and variation in the quality of water during the disassembly of oyster frames and fishery boxes. The result shows that the most important latent factors in the Tapeng Lagoon are the ocean factor, the primary productivity factor, and the fishery pollution factor. Canonical discriminant analysis is applied to identify the source of pollution in neighbouring rivers outside the Tapeng Lagoon. The two constructed discriminant functions (CDFs) showed a marked contribution to all the discriminant variables, and that total nitrogen, algae, dissolved oxygen, and total phosphate combined in the nutrient effect factor. The recognition capacities in these two CDFs were 95.6% and 4.4%, respectively. The water quality in the Kaoping river most strongly affected the water quality in the Tapeng Lagoon. Disassembling the oyster frames and fishery boxes improved the water quality markedly. However, environmental topographic conditions indicate that strengthening stream pollution prevention and constructing another entrance to the ocean are the best approaches for improving the quality of water in the Tapeng Lagoon by reducing eutrophication. These approaches and results yield useful information concerning habitat recovery and water resource management.