After decades of strict pollution control and municipal sewage treatment, the water quality of the Tanshui River increased significantly after pollution mitigation as indicated by the River Pollution Index (RPI). The pollution level of the estuarine region decreased from severe pollution to mostly moderately impaired. The most polluted waters are presently restricted to a flow track length between 15–35 km relative to the river mouth. From July 2011 to September 2012, four surveys of fish and benthic macroinvertebrates were conducted at 45 sampling sites around the Tanshui River basin. The pollution level of all the study area indicated by the RPI could also be explained by the Family Biotic Index (FBI) and Biotic Index (BI) from the benthic macroinvertebrate community, and the Index of Biotic Integrity (IBI) of the fish community. The result of canonical correlation analysis between aquatic environmental factors and community structure indicated that the community structure was closely related to the level of water pollution. Fish species richness in the estuarine area has increased significantly in recent years. Some catadromous fish and crustaceans could cross the moderate polluted water into the upstream freshwater, and have re-colonized their populations. The benthic macroinvertebrate community relying on the benthic substrate of the estuarine region is still very poor, and the water layer was still moderately polluted.

Aim: This study aimed to identify the optimal time and fishing methods for removing exotic fishes, including striped snakehead (Channa striata), marble goby (Oxyeleotris marmorata), tilapia (Oreochromis spp.), three-spot gourami (Trichopodus trichopterus), and predatory carp (Chanodichthys erythropterus), from Longluan Lake, which is located in Kenting National Park in Taiwan. Methodology: The selected fishing methods included lure fishing, longline fishing, and fyke netting. A total of 2,284 individuals were collected over 12 removal events in Longluan Lake from 2017 to 2019. Among the collected fish, 1,640 fish represented exotic species, and 644 fish represented native species. Results: Among the collected fish, 1,640 fish represented exotic species, and 644 fish represented native species. Based on the results of this study, we suggest that the optimal time for managing exotic fishes is from April to June, when is the period representing lower water levels in Longluan Lake. For removing specific exotic fish in Longluan Lake, employing lure fishing in natural habitat is effective for C. striata and Oreochromis spp., utilizing fyke netting in natural habitat is workable for T. trichopterus and C. erythropterus, and operating fyke netting in artificial habitat is useful for O. marmorata. Interpretation: The habitat preferences and sampling efficiency of gears vary among exotic fishes, however, a combination of applying lure fishing and fyke netting in both habitat types will achieve the greatest advantage for controlling exotic fishes in the Longluan Lake.