This study investigates the contamination of microplastics (MPs) and heavy metals in surficial sediments of the Pasig River, Philippines, during the wet season. This season, marked by heightened rainfall, runoff, and stormwater flow, potentially enhances the dispersion and accumulation of pollutants, leading to elevated pollution levels. MPs and heavy metals pose significant threats to aquatic ecosystems and human health, and their accumulation in river sediments warrants urgent attention. Samples were collected from multiple sites along the river, focusing on sediment composition, to analyze MP abundance and heavy metal concentrations. Results revealed high concentrations of MPs, predominantly polyester, polyethylene and acrylonitrile-butadiene copolymer, and heavy metals which were significantly higher in urbanized areas. MPs were found at all sampling locations, ranging from 2700 to 28,250 particles per kilogram of sediments. Heavy metals in the sediments varied, with concentrations of Cd (<0.003 mg/kg), Pb (3.09–50.48 mg/kg), Zn (53.37–175.74 mg/kg), and Fe (11,629–25,687 mg/kg), in the order Fe > Zn > Pb > Cd. According to the Hong Kong-Interim Sediment Quality Values criteria, the sediments were not contaminated by Cd, Pb, and Zn. Correlations between MP abundance and metals were found to be moderate for Pb and Zn but low for Fe, suggesting complex pollution dynamics. These findings emphasize the need for comprehensive monitoring and targeted waste management strategies to address MPs and heavy metal pollution, particularly during the wet season. Identifying MPs polymer types and their possible pollution sources provides valuable data to mitigate sediment contamination and protect aquatic ecosystems and human health.