- Due to the runtime flexibility offered by field programmable gate arrays (FPGAs), FPGAs are popular devices for stream processing systems, since many stream processing applications require runtime adaptability (i.e. throughput, data transformations, etc.). FPGAs can offer this adaptability through runtime assembly of stream processing systems that are decomposed into hardware modules. Runtime hardware module assembly consists of dynamic hardware module replacement and hardware module communication reconfiguration. In this paper, we architect a flexible base embedded system amenable to runtime assembly of stream processing systems using custom communication architecture with dynamic streaming channel establishment between hardware modules. We present a hardware module swapping methodology that replaces hardware modules without stream processing interruption. Finally, we formulate two design flows, system and application construction, to provide system and application designer assistan...