Since perfluoroalkyl acids (PFAs) are widely used and harmless to organisms, they have attracted great attention in recent years. e distribution of PFAs in the oceans all around the world is well documented. However, the study of PFAs in Xiamen could be a beneficial complement, for its unique geologies of no rivers that originate from other cities to influence the concentration of PFAs in this area. In this paper, six PFAs were analyzed in water, sediments, and organisms from both freshwater and seawater and the bioaccumulation factors (BAFs) were calculated with the quantity of PFAs in different trophic levels of aquatic organisms. e results showed that the ΣPFA concentrations ranged from 7.66 to 11.98 ng·L − 1 for seawater samples and from 2.12 to 8.61 ng·L − 1 for freshwater. e concentration of ΣPFAs in sediments was 7.43-12.89 ng·g − 1 and 4.53-5.80 ng·g − 1 in seawater and freshwater, respectively. e PFA concentration in water is highly positive correlated with the PFA concentration in sediments (R 2 � 0.85). e calculated bioaccumulation factors (BCFs) were 6412-14254 L·kg − 1 and 2927-7959 L·kg − 1 for perfluorooctanoic acid (PFOA) and perfluorooctane sulfonates (PFOS), respectively. PFOA seems more bioaccumulative than PFOS in seawater. e results illustrated the PFA pollution in the Xiamen sea area, and it is useful for the protection and control of the organic pollutants in this area.