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As newly formed landscapes evolve, physical and biological changes occur that are collectively known as primary succession. Although succession is a fundamental concept in ecology, it is poorly understood in the context of aquatic environments. The prevailing view is that lakes become more enriched in nutrients as they age, leading to increased biological production. Here we report the opposite pattern of lake development, observed from the water chemistry of lakes that formed at various times within the past 10,000 years during glacial retreat at Glacier Bay, Alaska. The lakes have grown more dilute and acidic with time, accumulated dissolved organic carbon and undergone a transient rise in nitrogen concentration, all as a result of successional changes in surrounding vegetation and soils. Similar trends are evident from fossil diatom stratigraphy of lake sediment cores. These results demonstrate a tight hydrologic coupling between terrestrial and aquatic environments during the colonization of newly deglaciated landscapes, and provide a conceptual basis for mechanisms of primary succession in boreal lake ecosystems.