Modern Intelligence, Surveillance and Reconnaissance (ISR) systems are increasingly being assembled from autonomous systems, so the resulting ISR system is a System of Systems (SoS). In order to take full advantage of the capabilities of the ISR SoS, the architecture and the design of these SoS should be able to facilitate the benefits inherent in a SoS approach - high resilience, higher level of adaptability and higher diversity, enabling on-demand system composition. The tasks performed by ISR SoS can well go beyond basic data acquisition, conditioning and communication as data processing can be easily integrated in the SoS. Such an ISR SoS can perform data fusion, classification and tracking (and conditional sensor tasking for additional data acquisition), these are extremely challenging tasks in this context, especially if the fusion is performed in a distributed manner. Our premise for the ISR SoS design and deployment is that the system is not designed as a complete system, where the capabilities of individual data providers are considered and the interaction paths, including communication channel capabilities, are specified at design time. Instead, we assume a loosely coupled SoS, where the data needs for a specific fusion task are described at a high level at design time and data providers (i.e., sensor systems) required for a specific fusion task are discovered dynamically at run time, the selection criteria for the data providers being the type and properties of data that can be provided by the specific data provider. The paper describes some of the aspects of a distributed ISR SoS design and implementation, bringing examples on both architectural design as well as on algorithm implementations.