Pollution in the marine environment has been a pressing issue for many years. The presence of microplastics in the sea poses numerous dangers. Firstly, it adversely affects marine ecosystems due to the ingestion of microplastics by various marine organisms such as fish, seabirds, and invertebrates. Additionally, microplastics have the capability to absorb and transport pollutants, thereby contributing to the chemical contamination of the oceans. Furthermore, there are risks to human health, as microplastics can accumulate in fish and other marine organisms consumed as part of the human diet, potentially exposing people to harmful chemicals. Currently, there have been limited efforts to collect microplastics, with rudimentary systems employed for seawater filtration. This paper proposes a novel approach to address this issue by designing a compact vehicle specifically tailored for microplastic collection in port areas of seas and river courses. To improve the efficiency of the design process, TRIZ methodology was used to overcome the non-avoidable technical contradictions encountered in the design of a filtering system for microplastics. For example, increased filtering efficiency results in increased energy consumption and decreased maneuverability of the drone, i.e., for one technical feature that improves there are others that get worse. TRIZ helped overcome these contradictions, find an innovative solution, and identify an optimal product architecture that meets the required technical specifications without resorting to compromise solutions. The proposed design entails a self-guided drone featuring a bi-hull structure equipped with two separate electrical circuits to power the motors and control unit. Positioned at the center of the drone’s lattice frame is an adjustable-height filter housing three collection nets, designed to ensure optimal and efficient water filtration. This novel approach not only addresses the immediate challenge of microplastic collection but also contributes to long-term environmental sustainability by reducing the ecological footprint of marine operations and supporting global initiatives for cleaner oceans.