Lake surface area in arctic and sub-arctic Alaska is changing in response to permafrost deterioration, changes in precipitation, and shifts in landscape hydrology. In interior Alaska, the National Park Service’s Central Alaska Network Shallow Lakes program studies lakes and ponds in a wide range of geomorphological settings ranging from alpine lakes to low lying lakes on fluvial plains. The purpose of this study was to determine if and how lake area was changing across this diverse environment. Using the USGS Dynamic Surface Water Extent product, we tested landscape-scale trends in surface water area from 2000–2019 in 32 distinct ecological areas, or ecological subsections, within the three parks. Surface water area declined in 9 subsections, largely in glaciated landscapes with coarse substrates and areas underlain by ice-rich permafrost. Surface water increase was seen in one subsection in the floodplain of the Copper River in Wrangell-St. Elias National Park. No net change was observed in many subsections, but individual lake analysis showed that within several ecological subsections some lakes were increasing in area while others decreased in area, masking changes in lake surface area within the subsection. Over the course of the study period, surface water area in all parks experienced similar fluctuations, likely due to oscillations in regional climate. Periods of high surface water area coincided with relatively warm, wet periods. Climate change models project increases in both temperature and precipitation in Alaska; our results suggest periods of regional wetting may mask longer-term declines in surface water area in some geomorphological settings. Overall, lake surface area declined over the study period; declines were greatest in the Glaciated Lowlands in Denali National Park and Preserve.