A continuously-operable flow stream processing system and method has two or more fluid processing media arranged in a fluid conduit network to provide alternate flow paths for a flow stream to be processed (e.g. filtered). Valves and other flow control devices, e.g. controller module and sensors, are used to redirect the flow stream from one or more service-needed fluid processing media to service-ready fluid processing media without taking the system offline to remove, repair, replace, clean in situ, or otherwise service the service-needed fluid processing media, so that the system may operate continuously to process the flow stream without stoppage. Redirection into alternative flow paths and media may be automatically implemented based on a predetermined threshold or trigger condition, such as may be detected by sensors directly or indirectly monitoring media condition.