We present simultaneous measurements of dissolved CO2, CH4 and N2O from lake, pond and low order fluvial systems across two summers (2016-2017) in the Indigirka River lowlands in northeast Siberia.Inland water sites were sampled in summer (late July to early September) of 2016 and 2017. In total, two small lakes (<3 m deep, 0.04 and 0.14 km2 in area), one thermokarst lake (up to 7 m deep, 0.51 km2, actively eroding into a Yedoma ridge), 24 pond sites (<0.5 m deep, 3-255 m2), and 11 fluvial sites along a ~5 m wide stream were sampled. Additionally, five locations of flooded tundra area were sampled in 2017. Water samples were collected from the thermokarst lake at five different locations around its shoreline, and from the two small lakes at 3-4 shoreline locations. Each site was sampled three times in the summers of 2016 and 2017. Each flooded tundra location was sampled four times in 2017. In-situ measurements of water temperature, pH, electrical conductivity (EC), water depth and surface area were collected during sample collection. Temperature and EC were measured with a Greisinger GMH 3431 meter (accuracy of ± 2 µs/cm and ± 0.2 K), pH was measured using an Eijkelkamp SAM 1 meter (accuracy of ± 0.01).