Anthropogenic activities have increased the concentrations of greenhouse gases in the atmosphere destabilizing global climate patterns. Together, carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) are responsible for over 70% of the increased radiative forcing of the atmosphere relative to pre-industrial levels. Identifying the sources of these gases is key to controlling their emissions. I investigated whether headwater streams are an important source of greenhouse gases to the atmosphere and how emission rates respond to anthropogenic land use.  Employing a variety of methods including 15N stable isotope tracer experiments, I demonstrated that N2O was produced in the sediments of headwater streams, and that production rates were correlated with stream water NO3- concentrations, an indicator of agricultural land use. At the basin scale, the streams had high areal N2O emission rates relative to soils, but only emitted about 5% of the N2O evading from soils due to the small total surface area of streams.  Although N2O emissions from streams have received more attention than CH4, I found that CH4 emissions induced by anthropogenic activity had a global warming potential 12 times that of N2O. Methane emission rates were highest in streams affected by agriculture and urbanization, likely because the accumulation of fine sediments in these streams promoted sediment anoxia and methane production.  In a separate line of research, I investigated the environmental fate and transport of a new class of chemical compounds (ionic liquids, ILs) that may replace traditional solvents that indirectly promote the accumulation of CH4 in the atmosphere. I found that ILs do not strongly sorb to aquatic sediments and are unlikely to bioaccumulate if released into aquatic ecosystems via industrial effluent.  My dissertation research demonstrates that headwater streams are sources of greenhouse gases to the atmosphere, but that N2O emissions have been overestimated while CH4 emissions have been overlooked. By linking in-stream CH4 and N2O production to specific effects of anthropogenic land use (e.g., nitrate enrichment and sedimentation), I have identified management actions that could be taken to reduce these emissions.