Streams, rivers, and other freshwater features may be significant sources of CH₄ to the atmosphere. However, high spatial and temporal variabilities hinder our ability to understand the underlying processes of CH₄ production and delivery to streams and also challenge the use of scaling approaches across large areas. We studied a stream having high geomorphic variability to assess the underlying scale of CH₄ spatial variability and to examine whether the physical structure of a stream can explain the variation in surface CH₄. A combination of high-resolution CH₄ mapping, a survey of groundwater CH₄ concentrations, quantitative analysis of methanogen DNA, and sediment CH₄ production potentials illustrates the spatial and geomorphic controls on CH₄ emissions to the atmosphere. We observed significant spatial clustering with high CH₄ concentrations in organic-rich stream reaches and lake transitions. These sites were also enriched in the methane-producing mcrA gene and had highest CH₄ production rates in the laboratory. In contrast, mineral-rich reaches had significantly lower concentrations and had lesser abundances of mcrA. Strong relationships between CH₄and the physical structure of this aquatic system, along with high spatial variability, suggest that future investigations will benefit from viewing streams as landscapes, as opposed to ecosystems simply embedded in larger terrestrial mosaics. In light of such high spatial variability, we recommend that future workers evaluate stream networks first by using similar spatial tools in order to build effective sampling programs.