Monitoring complex distributed and heterogeneous systems such as cyber-physical or internet-of-things systems is challenging. Different kinds of information must be aggregated in a flexible manner to provide an overview on the actual state of the system. Recently, even heterogeneous Big Data systems have been proposed, which integrate classical server machines and hardware co-processors, such as Graphical Processing Units. In this paper, we present a system-level monitoring approach for a heterogeneous Big Data streaming system. We discuss the requirements stemming from a recent research project, a solution architecture and discuss experiences and promising results from preliminary experiments with the realization.