The area beneath a river where surface water mixes with groundwater (the hyporheic zone), is an important biogeochemical reactor, providing a variety of ecosystem services. In addition to hosting ecologically and economically important microbial processes, it is subject to dynamics in terms of inputs from the surface. In chapter 2, I explore the ways in which hyporheic zone dissolved oxygen conditions respond to surface channel flow perturbations. I show that the surface channel flow velocity exerts a strong influence on hyporheic dissolved oxygen conditions, that there is lag between surface channel flow perturbations and response in the hyporheic zone, that the response has memory and depends on direction, and that even in a homogenous riverbed, temporal fluctuations in flow can give rise to small areas of anomalous redox conditions, also known as redox microzones. In chapter 3, I explore the hyporheic microbiome, with the intent of understanding how variations in hyporheic redox conditions influence spatial patterns of microbial community structure, and how the flume’s microbiome compares to a natural hyporheic microbiome. I find that while the flume’s microbiome is not identical to natural hyporheic systems, it bears significant similarity, and is more similar to hyporheic systems than it is to other environments. I also show that the flume microbiome is at least partly controlled by the presence or absence of oxygen within the sediments. In chapter 4, I explore the reactive tracer resazurin and its use for measuring respiration. I explore the molar ratio between resazurin conversion and respiration, and how this can be used to quantify hyporheic respiration rates in real-world systems. Finally, in chapter 5, I show a few interesting oddities observed over 5 years of flume experiments. Taken together, this work represents a step forward in the understanding of the dynamic and complex way the hyporheic zone works.