This work investigated water samples collected from Tapeng Lagoon, Taiwan. Factor analysis was conducted to explain the characteristics and the 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 Tapeng Lagoon are the ocean factor, primary productivity factor, and the fishery pollution factor. Canonical discriminant analysis is applied to identify the source of pollution in neighboring rivers outside Tapeng Lagoon. The two constructed discriminant functions (CDFs) showed markedly contribution to all 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%, 4.4%, respectively. The water quality in the Kaoping river most strongly determined that in the Tapeng Lagoon the best is. And disassembling the oyster frames and fishery boxes improves the water quality markedly. However, environmental topographic conditions indicate that strengthening stream pollution prevention and to constructing another entrance to the ocean are the best approaches for improving the quality of water in Tapeng Lagoon, especially by reducing eutrophication. These approaches and results yield useful information concerning habitat recovery and water resource management.