Uncertainty about controls on long-term carbon and nitrogen balance, turnover, and isotopic signature currently limits our ability to predict ecosystem response to disturbance and landscape change. We used a two-century, post-glacial chronosequence in Glacier Bay, Alaska to explore the influence of carbon and nitrogen dynamics on soil and leaf stable isotopes. Carbon dynamics were closely linked to soil hydrology, with increasing soil water retention during ecosystem development resulting in a linear decrease in foliar and soil δ13C, independent of shifts in vegetation cover and despite constant precipitation across sites. Conversely, nitrogen dynamics responded to interactions between soil development, vegetation type, microbial community, and topography. Contrary to the predictions of nutrient retention theory, potential nitrification and denitrification were high virtually from the beginning of the chronosequence and gaseous and hydrological N losses were highest at mid-successional sites, 140 to 165 years since deglaciation. Though leaching of dissolved nitrogen is considered the predominant pathway of nitrogen loss at high latitudes, we found that gaseous nitrogen loss was more tightly correlated with δ15N enrichment. These results suggest that δ13C in leaves and soil can depend as much on soil development and associated water availability as on climate, and that nitrogen availability and export depend on interactions between topography, soil development, vegetation type, and microbial activity.