Boreal wetland carbon cycling is vulnerable to climate change in part because hydrology and the extent of frozen ground have strong influences on plant and microbial functions. We examined the response of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) across an experimental manipulation of water table position (both raised and lowered water table treatments) in a boreal-rich fen in interior Alaska. DOC and TDN responses to water table manipulation exhibited an interaction with seasonal ice dynamics. We observed consistently higher DOC and TDN concentrations in the lowered water table treatment (71.7 ± 6.5 and 3.0 ± 0.3 mg−L) than in both the control (55.6 ± 5.1 and 2.3 ± 0.2 mg−L) and raised (49.1 ± 4.3 and 1.9 ± 0.1 mg L−1, respectively) water table treatments. Across all plots, pore water DOC concentrations at 20 cm increased as the depth to water table increased (R2 = 0.43, p < 0.001). DOC concentrations also increased as the seasonal thaw depth increased, with solutes increasing most rapidly in the drained plot (R2 = 0.62, p < 0.001). About half of the TDN pool was composed of dissolved organic N (DON). Inorganic N and DON were both highly correlated with changes in DOC, and their respective constraints to mineralization are discussed. These results demonstrate that a declining water table position and dryer conditions affect thaw depth and peat temperatures, and interactions among these ecosystem properties will likely increase DOC and TDN loading and potential for export in these systems.