Eastern part of Segara Anakan Lagoon (E-SAL) is an estuarine ecosystem to dispose industrial waste i.e. lead (Pb) containing waste. The study aims to analysis the distribution of Pb in soil, water and mangrove vegetation matrices. Several parameters including bioaccumulation factor (BAF), translocation factor (TF), leaf morphometric (the effect of Pb for mangrove vegetation) were used to estimate their impact. We developed a pre-design of mangrove zone as a model in reducing Pb cntaminantion in E-SAL. The results showed the distribution of Pb in E-SAL was 0.177 -0.233 mg/L (water), 0.320 -0.780 mg/kg (soil), 4.80-8.67 mg/kg (mangrove root), 2.48-6.96 mg/kg (mangrove stem), and 1.48-4.76 mg/kg (mangrove leaf). The scoring of BAF in mangrove vegetation had value between 22.2-40.1 and TF between 0.9-1.3. The distribution of Pb in soil depths were 8.89 mg/kg (0-50 cm) to 0.56 mg/kg (150-200 cm). The impact of Pb was 2-60 % of leaf damage on surface leafs. The mangrove zone to reduce impact of Pb in E-SAL was Rhizophora apiculata, Bruguiera sexangula, Aegiceras corniculatum and Sonneratia caseolaris as mangrove species in the first zone.