This paper presents an embedded hardware/software implementation for the computing system of a small scale unmanned autonomous sailing boat. The system is integrated in a single XILINX FPGA, and hosts a Microblaze soft processor surrounded with heterogeneous, custom designed, control and processing modules than handle the interface with all the sensors, actuators and communication devices of the sailing boat. These interfacing modules implement tasks that have been decentralized from the main processor, thus alleviating its computational load and providing processing time for higher level software applications. Using an FPGA to implement an integrated single-chip computing system, as an alternative to conventional processors, has proven to be a very flexible solution as it eases the migration of computation tasks between the hardware and software domains, and more importantly, allowing the rapid adaptation of the digital interfacing hardware in order to support additional peripheral devices required for an application mission. The software component of the boat's control system runs on the top of the uClinux embedded operating system and is formed by various concurrent applications developed in C with the standard Linux libraries. The remote monitoring, configuration and operation of the sailing boat is done via a WiFi link, using a graphics interactive application that runs on a conventional PC.