Historically, stream ecology was formed on the basis of measuring how much organic matter rivers move downstream, and the “processing continuum” as this organic material is alternatively deposited, processed, and further transported. A significant amount of material is continuously exported from headwater streams, and via advection can be moved long distances downstream prior to processing. Along the way, these materials exchange rapidly between the water column and streambed, migrating downstream in alternating deposition and resuspension events called saltation, and are influenced by complexity in the physical and biologically template of stream structure. A new focus in ecology is understanding how “novel materials” are transported, retained, and persist in stream and river ecosystems. Despite many potential controls over material transport in streams and rivers, we often treat the transport of these materials as a homogenous process in the environment because we lack empirical observations addressing the complexity inherent in natural systems. Therefore, the overarching objective of my dissertation is to improve understanding of the transport, retention, and persistence of two novel materials that are actively transported by flowing waters using a combination of empirical and modeling approaches, spanning lab to watershed experimental scales. More specifically, I investigate the dynamics and transport of two novel materials: environmental DNA (eDNA) and a genetically modified protein (Cry1Ab).