In order to power remote sensors and/or data transmission devices in an aquatic environment, sedimentary microbial fuel cells and floating microbial fuel cells have been proposed in the literature, representing a continuous source of renewable and sustainable energy. However, both classes of devices are characterized by large dimensions and are immobilized in the environment within which they are working. Accordingly, when portability and small dimensions are strict requirements, these configurations cannot be exploited. The present work proposes a novel, compact and cost-effective floating set-up based on small-scale microbial fuel cells. A method for in situ anodic biofilm formation was validated through experiments conducted in laboratory and in a real marine environment. Carbon felt-based anodic electrodes were used to build different replicas of floating microbial fuel cells. Their overall performance was evaluated during two field measurement campaigns carried out in the Mediterranean Sea. The study demonstrated a high stability of the floating microbial fuel cells even in a real, uncontrolled environment. The devices were able to continuously produce electricity using seawater as fuel and electrolyte. This study suggests that these devices can be used as portable power supplies for sensors in a complex environment such as the open sea due to the easy preparation of anodic electrodes, together with the simple architecture of floating microbial fuel cells.