Abstract: according to the water quality monitoring results of three seasons(rainy season、average water season and dry season) in Ma'an Archipelago area in 2012~2013, we analyse the degree of water quality eutrophication and organic pollution by using eutrophication index (E), quality of nutrition state index (NQI) and organic pollution index (A). The results show that: the content of COD and DO meet the first category of water quality standards, the content of DIP basically meets the second category of water quality standards, while the content of DIN exceeds the standards seriously. In rainy and average water season, the difference of each evaluation content is obvious, while in dry season is nearly close. Eutrophication and organic pollution are serious, different seasons turn out to be eutrophic, organic pollution is in moderate state in average water season and dry season, while it is heavily polluted in rainy season, that is rainy season average water season dry season. Look from the partition, water eutrophication and organic pollution in the midwest are the most serious in functional B、C、D partitions, north coastal water in A partition (grouper resource reserve) is in moderate pollution state, while the southeast coastal water in E partition(ecological culture zone) is the lightest.