Lead (Pb) is a non-essential heavy metal found as an inorganic pollutant in the water, sediment, and mangrove plant tissue in Wonorejo River Estuary. Several studies showed that its concentration exceeds the quality standard stipulated in the Indonesian Government Regulation Number 22 of 2021 and the EPA sediment quality. Moreover, the phytoremediation of Pb through mangroves Avicennia alba, Rhizophora stylosa, Sonneratia caseolaris, and Avicennia marina at Wonorejo River Estuary was investigated. It was discovered that the environmental factors such as temperature, pH, and salinity as well as Bioconcentration Factor (BCF) and Translocation Factor (TF) values are different for each species. The dynamics of the Pb phytoremediation system were also modeled using Vensim PLE x64 software to determine the effect of environmental factors such as temperature, pH, salinity, BOD and COD, as well as Pb concentration on the ability of mangroves to accumulate and translocate Pb. The results showed that a behavioral mechanism pattern was formed based on the relationship between the environmental factors, Pb concentration, and the phytoremediation ability of the mangroves with time. This pattern affected the root and leaf BCF values of each mangrove. Furthermore, the validation test showed that the model is structurally valid and has MAPE values for the Pb phytoremediation model with S. caseolaris and R. stylosa having <30% while Avicennia marina and A. alba had <50%. Therefore, the model was categorized as fairly good with a valid forecast. The system dynamics predicted that the highest concentrations of Pb in water, roots, and stems in 2041 were in R. stylose at 1,329,110 mg/L, 2,054,110 mg/kg, and 3,393,950 mg/kg, respectively. The highest accumulation value in plant tissue was dominated by mangrove species of R. stylose. In conclusion, the environmental parameter values at habitat of R. stylose were in good condition for the growth of the mangroves compared with other species of mangrove.