This study provides a baseline analysis of sediment pollution in Kalmar Guest Harbor, Sweden, focusing on metals and microplastics. The study site, a bustling coastal area, was chosen to investigate the connections between anthropogenic activities, bioturbation, and environmental contaminants. The results revealed that the pollution extends beyond 30 cm of depth below the seafloor, with elevated levels of copper (Cu), tungsten (W), cadmium (Cd), zinc (Zn), lead (Pb), and microplastics. Significantly, there is no previous publication alarming the W contamination in the Baltic Sea sediment, and therefore, our findings highlight the need for further investigation into tungsten contamination in the region. Furthermore, we explored the distribution patterns, potential sources and relationships of different contaminants. The K-means cluster analysis revealed that bioturbation is speculated to influences the depth concentration of pollutants, particularly at shallow depths (0‬–18 cm). Metal contaminants do not appear to be predominantly bound to MP particles.