Understanding the vertical distribution of heavy metals aids in tracing the contamination history, however, it is limited for mangrove-dominated river. Thus, this study aimed to assess the vertical distribution of nine heavy metals and their possible ecological risk in several layers of core sediments from a mangrove-dominated river inside the Sundarban mangrove forest (World heritage and Ramsar site), Bangladesh. 45 core samples from five stations were analyzed using Flame Atomic Absorption Spectrophotometer (FAAS). The findings showed that, with the exception of Fe, Ni, and Cu, which suggested increased metal release in recent times, higher metal levels were recorded in the surface layer (0–10 cm), followed by the middle layer (10–20 cm), and inner layer (20–30 cm) of sediment cores. When compared to non-industrial forest sediment, core sediment from industrial sites contained noticeably more metals (p < 0.05). Overall, the mean metal concentration (mg/kg) followed the increasing order of Cd < As < Pb < Cu < Cr < Zn < Ni < Mn < Fe. Among the studied metals, the levels of Cd and Ni exceeded the average shale value. Contamination indices such as enrichment factor (EF), contamination factor (CF), and geo-accumulation index (Igeo) showed that the studied sediments were only contaminated by Cd. Ecological risk assessed by ecological risk factor (Ei r) and risk index (RI) suggested that the analyzed heavy metals, with the exception of Cd, posed no significant ecological threats. All of the heavy metals analyzed might have originated from similar anthropogenic sources, according to the correlation matrix, cluster analysis (CA), and principal component analysis (PCA).