This work presents a new microwave sensor integrated with a microfluidic channel to allow real-time microplastics detection in aqueous environments. The microfluidic channel has a diameter of 700 μm, carrying water and microplastics with a diameter of 400 μm. The microwave sensor is a printed microwave resonator operating at 3.58 GHz, measured in continuous wave to detect the presence of microplastics. It operates by concentrating a reactive evanescent field that decays by −3 dB at a distance of 3 μm at the sensitive zone, not being limited by the Rayleigh diffraction. Simulations show that the best operation frequency lays 10 MHz apart from the sensor’s resonant frequency. Additionally, it was shown that to distinguish two microplastics, they should be separated by at least 4.2 mm. Experimental results show the ability of detecting microplastics with size down to 400 μm, through a power reflection of 180 μW in amplitude. The single frequency measurements allowed a microfluidics throughput of 100 μl/min, with room for improvements with higher bandwidth readout electronics.