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The construction of a new highway between Uppsala and Mehedeby in northern Uppland, southeastern Sweden, has motivated extensive archaeological excavations. To describe changes in shoreline configuration over time, the isolation of nine lake basins has been interpreted from diatom analysis. Their isolation ages were determined from 45 AMS radiocarbon dates (five per site) of terrestrial macrofossils, mainly Betula and Alnus seeds. The isolation ages and the corresponding altitudes indicate a complicated pattern of isostatic uplift during the late Holocene. Neither the present-day isobases nor those for the ‘Neolithic Sea’ seem to explain their isolation ages and corresponding altitudes in relation to their geographic distribution. Since at least some of the lakes are situated in a relatively pronounced topographic landscape we are inclined to explain the observations as the result of small-scale irregular uplift. Earthquakes are rare in the area at present suggesting short-term tectonic activities along existing fault lines.