Summary Tundra ponds are a dominant feature on the Arctic Coastal Plain, but their response to warming, especially in the long‐term, is largely unknown. Our study assessed changes in algal nutrient limitation over a 40‐year period in historically studied ponds that may have been affected by either human development in the region or increased temperatures leading to permafrost thaw and nutrient release. We also compared nutrient limitation of algae in the pelagic and benthic zones at a landscape level. Nutrient diffusing substrata (NDS) and bottled nutrient incubations, which expose natural algal communities to known quantities of nitrogen (N) and phosphorus (P), were utilised to determine benthic and phytoplankton algal nutrient limitation, respectively, in a series of ponds on the north slope of Alaska, USA. This included ponds where phytoplankton nutrient limitation was examined in 1971–1973 as part of the International Biological Program (IBP), as well as ponds in a remote protected area and others near the village of Barrow. Nutrient limitation status of phytoplankton has changed since the original IBP study 40 years ago from P limitation to NP co‐limitation. One‐third of regional phytoplankton enrichment experiments indicated no nutrient limitation of algal growth, and none exhibited single‐nutrient P limitation. This shift in nutrient limitation was coincident with increased water column nutrients due to degrading permafrost, and to the expansion into the ponds of macrophytes, which may compete with algae for available nitrogen. A comparison of pelagic and benthic experiments across the landscape revealed differences among these zones with a predominance of NP limitation of phytoplankton and absence of nutrient limitation in the benthic zone, reflecting contrasting nutrient limitation status within the same ponds. Permafrost thaw is probably reintroducing previously frozen stores of P or N to the sediment surface, which are quickly taken up by periphyton but become limited in the water column. Grazing by invertebrates, which were not excluded from the benthic assays, may also have influenced the results. While ponds within the village of Barrow had higher nutrient and algae levels, there was no obvious effect of urban development on nutrient limitation status, nor did development appear to have influenced the historic IBP pond sites.