Heavy metal pollution in coastal waters has emerged as a significant environmental concern, particularly near river estuaries and urban areas, due to uncontrolled industrial, mining, and domestic activities. This study aimed to assess the spatial distribution of heavy metals (cadmium, iron, lead, and aluminum) and the corresponding bacterial community structures at Sendangbiru Beach, Malang, Indonesia. The methods employed included heavy metal concentration analysis using Atomic Absorption Spectrophotometry (AAS) and evaluation of bacterial community structures through environmental DNA (eDNA) metabarcoding. Results revealed that iron (Fe) exhibited the highest concentrations, suggesting significant anthropogenic and natural inputs. Cadmium (Cd) and lead (Pb) showed lower but consistently distributed levels, indicating chronic pollution from human activities. Metagenomic profiling identified diverse bacterial genera, notably Psychrobacter, Neptunomonas, and Pseudomonas, known for their resistance to heavy metal contamination. High microbial diversity indices at specific sites, such as Waru-Waru and Watu Pecah, indicated ecological resilience and adaptability in response to environmental stressors. These findings highlight the effectiveness of integrating eDNA metabarcoding with geospatial analyses as a valuable tool for monitoring ecological health and guiding sustainable coastal ecosystem management.