Segara Anakan is a coastal lagoon located in south central Java,Indonesia,where large mangrove areas are still observed.In recent decades,this lagoon has undergone major effects of anthropogenic activities,such as the increase of the urban area,industries wastes,sewage disposal,aquaculture and agricultural activities,which are probably altering heavy metals biogeochemical cycles in this ecosystem.In order to study the spatial distribution of heavy metals within the lagoon 29 sediment samples were collected.The samples were manually collected with the help of a stainless steel spoon and storage in plastic bags until reaches the laboratory where they were frozen until analysis.A strong acid chemical extraction(HNO3 + HCl,3:1)was performed in microwave oven and subsequently determination of metals by ICP/EAS(Al,Fe,Mn,Cu,Ni,Cr,Co,Pb and Zn).The average metal concentration was: iron 52.6 mg.g-1(± 6.9 mg.g-1); aluminum 28.8 mg.g-1(± 5.4 mg.g-1); manganese 1084 μg.g-1(± 424 μg.g-1); chromium 115 μg.g-1(± 21 μg.g-1); lead 95 μg.g-1(± 11 μg.g-1); zinc 69 μg.g-1(± 15 μg.g-1); copper 45 μg.g-1(± 21 μg.g-1); Ni 33 μg.g-1(± 7 μg.g-1)and Co 27 μg.g-1(± 5 μg.g-1).The highest concentrations of Co,Mn,Ni and Fe were observed in the sediments collected outside of the lagoon in the area where the lagoon reaches the sea.This trend is probably due to the high hydrodynamics present in the more industrialized area of the lagoon,that is probably responsible for the fine particles and associated metals transport to the marine areas near where the lagoon reached the sea.Aluminum,copper and lead presented higher concentrations in the more preserved area of the lagoon where large mangroves areas were observed.This area presented distinct metal sources that in association with lower hydrodynamics and higher water mass residence time that probably explain these metals concentrations.The highest Cr and Zn concentrations were observed in the area where the lagoon receives the input of the Citanduy river that drain a large agricultural area.The large use of Pesticides and herbicides in these large agricultural areas are probably the explanation of the higher Cr and Zn concentrations observed in these sediments.When comparing the observed metal concentrations with the average shale,contaminated and pristine sediment concentrations from the literature it was possible to observe that sediments can be considered as contaminated by Pb and Cr.