In this research, we primarily sample the microorganism, algae, fish, shrimp, crab and benthonic organism at all monitoring site. We analyse data to understand the species diversity index of the fish, aquatic insect and algae. We finally integrate each biological indicator to determine the water quality rank and take advantage of this to know whether the renovation of Dan-Shaei river was improved. Population density of micro-organism was low in Da-Han stream upper than Da-Si township, we have less total plate count, coliform and E. coli. The area range from Wu-ling bridge to Dou-Dou-Shih-Jie, total plate count and coliform of stream water increased conspicuously. In Dan-Shaei river, the population density of micro-organism was higher in the region between Sin-dian stream and Da-Han stream converge site, and from here down to Er-Chong flooding canal converge site. In this study, 295 taxa of algae were found from the collection of phytoplankton and periphyton. There were 29 taxa of cynobacteria, 141 taxa of diatom, 118 taxa of green algae, 5 taxa of euglenophytan and 2 taxa of dinoflagellate. The GI index derived from algae community indicated the downstream area was highly polluted in general. In one year of collection from Da-Han stream and Dan-Shaei river, 74 species belong to 35 family of fishes were found in 2009. In Da-Han stream, we had 35 species of fishes, non-tidal effected area from Si-Jhon bridge to Hou-Cun-jyun water collection site with 31 species, the tidal effected region from Chen-Lin bridge to Sin-Hai bridge with 7 species. Between Chen-Lin bridge and Sin-Hai bridge Megalops cyprinoides was common species and Mugil cephalus only can collected from the converge site. Dan-Shaei river was tidal effected from Sin-Dian stream and Da-Han stream converge site down to river mouth to Taiwan strait, we had 43 species of fishes in 2009, 12 species were new records, Mugil cephalus was the most common species. The benthic macroinvertebrate collected from Da-Han stream and Dan-Shaei river in 2009 total with 23,214 individuals belong to 89 taxa. The species diversity was higher in Da-Han stream than Dan-Shaei river. Non -tidal effected Da-Han upstream with more aquatic insect than the other area, tidal effected region only have pollution tolerant species such as annelid. The species richness in Dan-Shaei river lower than Da-Han stream, macroincertebrate community dominated with pollution tolerant annelid and crustacean. Dan-Shaei river sytem in 2008 and 2009, water quality indicated by IBI, FBI, EPT and BI, the most polluted area of tidal-effected region was from Chen-Lin bridge to Da-Han river mouth, the most clean water was in the area range between Jhou-Mei express way entrance and river mouth to Taiwan strait. The most polluted area of no-tidal effected region was from Chang-An bridge to Ruri-Fang of Keelung river, the most clean water was in the area range between Nan-Shih stream and Bei-Shih stream converge site dowm to Bi-Tan of Sin-Dian stream. The water quality of Da-Han stream from Si-Jhon bridge to Yuan-Shan-Yan is similar to upstream of Sin-Dian stream. Biological community of Dan-Shaei river system with diversity increased from 2005 to 2009 gradually, the fish community with more species and higher population density. In this study from 2008 and 2009, we have fish species records more than ever before. In the mean time, the most polluted area of Dan-Shaei river system only at downstream of Da-Han stream. The other region except Da-Han downstream, the pollution was lower down from worst to more easy state.