The abundant lakes dotting arctic deltas are hotspots of methane emissions and biogeochemical activity, but seasonal variability in lake extents introduces uncertainty in estimates of lacustrine carbon emissions, typically performed at annual or longer time scales. To characterize variability in lake extents, we analyzed summertime lake area loss (i.e., shrinkage) on two deltas over the past 20 years, using Landsat‐derived water masks. We find that monthly shrinkage rates have a pronounced structured variability around the channel network with the shrinkage rate systematically decreasing farther away from the channels. This pattern of shrinkage is predominantly attributed to a deeper active layer enhancing near‐surface connectivity and storage and greater vegetation density closer to the channels leading to increased evapotranspiration rates. This shrinkage signal, easily extracted from remote sensing observations, may offer the means to constrain estimates of lacustrine methane emissions and to develop process‐based estimates of depth to permafrost on arctic deltas.