We present a newly developed design for a self-contained, open-bottom benthic chamber for conducting in situ ecosystem experiments in streams, with a focus on biogeochemical processes like ecosystem metabolism and nutrient cycling. Our design is complementary to smaller, portable chamber designs, and is meant to answer questions at larger scales. These new chambers allow for a high level of experimental control in the field and can be used to generate spatially explicit data regarding ecosystem processes and to test mechanistic hypotheses. They are built to be deployed within the stream over periods of weeks to months and to withstand natural hydraulic forces of the benthic zone. We briefly summarize the materials and steps that are needed to construct these chambers. Then, we report the methods and results of a multi-part, diagnostic field study meant to demonstrate the performance and utility of the design. We quantified solute dynamics using a conservative tracer injection, then we estimated spatial variation in ecosystem metabolism and performed nutrient additions across the study site. The field study revealed that both flow velocity and water depth impose limitations on these chambers due to their open-bottom design and large size, but with appropriate methodological forethought these limitations can be minimized. We conclude with examples from a series of previous and ongoing studies demonstrating the application of our methodology in the field. The capacity of our design to accommodate complex, three-dimensional habitats and macrofauna, along with the capability to generate spatially explicit data, are the main advances that this methodology presents. These advances provide a novel method whereby motivated users can connect mechanistic hypothesis testing with natural ecological processes through ecosystem-level field experiments.