Stream ecosystems are actively involved in the biogeochemical cycling of carbon (C) and nitrogen (N) from terrestrial and aquatic sources. Streams hydrologically connected to peatland soils are suggested to receive significant quantities of particulate, dissolved, and gaseous C and N species, which directly enhance losses of greenhouse gases (GHGs), i.e., carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), and fuel in-stream GHG production. However, riverine GHG concentrations and emissions are highly dynamic due to temporally and spatially variable hydrological, meteorological, and biogeochemical conditions. In this study, we present a complete GHG monitoring system in a peatland stream, which can continuously measure dissolved GHG concentrations and allows to infer gaseous fluxes between the stream and the atmosphere and discuss the results from March 31 to August 25 at variable hydrological conditions during a cool spring and warm summer period. Stream water was continuously pumped into a water-air equilibration chamber, with the equilibrated and actively dried gas phase being measured with two GHG analyzers for CO2 and N2O and CH4 based on Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS) and Non-Dispersive Infra-Red (NDIR) spectroscopy, respectively. GHG measurements were performed continuously with only shorter measurement interruptions, mostly following a regular maintenance program. The results showed strong dynamics of GHGs with hourly mean concentrations up to 9959.1, 1478.6, and 9.9 parts per million (ppm) and emissions up to 313.89, 1.17, and 0.40 mg C or N m−2h−1 for CO2, CH4, and N2O, respectively. Significantly higher GHG concentrations and emissions were observed shortly after intense precipitation events at increasing stream water levels, contributing 59% to the total GHG budget of 762.2 g m−2 CO2-equivalents (CO2-eq). The GHG data indicated a constantly strong terrestrial signal from peatland pore waters, with high concentrations of dissolved GHGs being flushed into the stream water after precipitation. During drier periods, CO2 and CH4 dynamics were strongly influenced by in-stream metabolism. Continuous and high-frequency GHG data are needed to assess short- and long-term dynamics in stream ecosystems and for improved source partitioning between in-situ and ex-situ production.