Quantification of the present and future contribution to atmospheric methane (CH4) from lakes, wetlands, fluvial systems, and, potentially, coastal waters remains an important unfinished task for balancing the global CH4 budget. Discriminating between these sources is crucial, especially across climate-sensitive Arctic and subarctic landscapes and waters. Yet basic underlying uncertainties remain, in such areas as total wetland area and definitions of wetlands, which can lead to conflation of wetlands and small ponds in regional studies. We discuss how in situ sampling choices, remote sensing limitations, and isotopic signature overlaps can lead to unintentional double-counting of CH4 emissions and proposethat this double-counting can explain a pan-Arctic bottom-up estimate from published sources, 59.7 Tg yr-1(range 36.9–89.4 Tg yr-1) greatly exceeding the most recent top-down inverse modeled estimate of thepan-Arctic CH4 budget (235 Tg yr-1).