We measured microplastics [(MPs): 10 μm -5 mm] in untreated and secondary-treated sewage, highway runoff, and estuarine water in Tokyo, Japan, during both dry and wet weather. MPs smaller than 200 μm were predominant, making up > 60% of the total number, in all our water samples. The abundance of the MPs was 420 pieces / L in the influent and 8.7 pieces / L in the secondary effluent, indicating a removal efficiency of 98% during primary + secondary treatment. Of the measured polymers-polyethylene (PE), polypropylene, polystyrene, polyethyleneterephthalate (PET), polyethylene polypropylene copolymer, polyethylene polypropylene diene (PEPD), polyethylene vinyl acetate, and acrylonitrile styrene, PET was predominant in the sewage influent (88%) and effluent (49%) and its form was mostly fibrous, indicating contribution from laundry effluents. Highway runoff water samples contained high concentrations of MP (81-292 pieces / L). The highway runoff contained more PE (25%-49%) and PEPD (13%-30%) than PET (3%-12%) indicating contribution from debris from automobile tire wear and plastics weathered on the ground. MP concentrations in estuarine water samples were lower (1.4 -2.3 pieces / L in dry weather), and PET was predominant, at 52%-77%, indicating a dominant contribution from sewage effluent. Following rainfall, MP concentrations in the estuarine water increased to 1.8-4.3 pieces / L, and PEPD, in particular, increased significantly, with a proportion of 43%-52%, indicating the contribution of MPs derived from street runoff. Although analyses of molecular markers of sewage, i.e., linear alkylbenzenes and coprostanol, confirmed the input of combined sewer overflow (CSO) to the estuarine water, we did not observe any significant increase in PET fiber MPs, indicating that there was no significant increase in the contribution of MPs from sewage including CSO to the estuarine waters after a rain event. This study highlights the importance of street runoff as a source of MPs in urban aquatic environments. Further investigation should be performed to quantitatively access the individual sources and processes.