Streams and rivers are active processors of carbon, leading to significant emissions of CO₂ and possibly CH₄ to the atmosphere. Patterns and controls of CH₄ in fluvial ecosystems remain relatively poorly understood. Furthermore, little is known regarding how major human impacts to fluvial ecosystems may be transforming their role as CH₄ producers and emitters. Here, we examine the consequences of two distinct ecosystem changes as a result of human land use: increased nutrient loading (primarily as nitrate), and increased sediment loading and deposition of fine particles in the benthic zone. We did not find support for the hypothesis that enhanced nitrate loading down-regulates methane production via thermodynamic or toxic effects. We did find strong evidence that increased sedimentation and enhanced organic matter content of the benthos lead to greater methane production (diffusive + ebullitive flux) relative to pristine fluvial systems in northern Wisconsin (upper Midwest, USA). Overall, streams in a human-dominated landscape of southern Wisconsin were major regional sources of CH₄ to the atmosphere, equivalent to ~20% of dairy cattle emissions, or ~50% of a landfill’s annual emissions. We suggest that restoration of the benthic environment (reduced fine deposits) could lead to reduced CH₄ emissions, while decreasing nutrient loading is likely to have limited impacts to this ecosystem process.