Assessment of elemental contamination is emerging research in the present world. Metals are hazardous to the environment and people's health when metals concentration might exceed the tolerable level. In this research, 12 elements (i.e., Mn, Ni, Cu, Zn, As, Se, Sr, Co, Pb, Fe, Rb, and Ti) were assessed using the energy dispersive X-ray fluorescence (EDXRF) method in water and sediment samples in four (4) different spawning grounds of Tenualosha ilisha at the confluence of the Meghna River in Bangladesh. A comparative analysis was performed for the first time among four sampling spots, i.e., Chandpur, Bhola, Sandwip, and Hatiya, assessed all possible risk indices-it is a unique thing. Several risk indices were solved to determine the degree of sediment pollution for all 12 elements, e.g., degree of contamination (Cd):6.5–7.01, the modified degree of contamination (mCd): approximately 0.7, the pollution load index (PLI): 0.45–0.51, etc. where all the indices' results showed low or baseline levels of pollution. According to the enrichment factor (EF) computation, slight enrichment of examined metals except Pb and Zn was found. In addition to these, the ecological risk factor (Er) found in the following order (pollution level: low): Cu > Pb > Zn among the four stations. Moreover, a spatial incline of metal accumulation was observed among the four spots: Bhola < Sandwip < Hatiya < Chandpur based on the risk index (RI) set value. However, a strong positive correlation (p < 0.05) between Ca and Fe, Ti and Fe, Ti and Mn, Mn and Fe, Fe and Sr were observed while Ca, and Co were strongly negatively correlated (r = minus (-)0.60, p < 0.05). The cluster analysis was performed and got an asymmetrical cluster among the sampling stations. This study recommends assessing the heavy metal concentration in biological samples, particularly in Hilsha fish.