Lakes are significant contributors to global sources of greenhouse gases (GHGs), estimated to emit 20% the equivalent carbon dioxide (CO2) produced via fossil fuels, and 10-20% of natural methane (CH4) emissions. Although approximately 50% of all lakes are distributed in high latitudes, a critical lack of studies in High Arctic environments represents a major gap in our understanding of lakes in the global carbon cycle. Compounding this, morphological variability of larger, often irregular lakes, may lead to heterogenous GHG production throughout. However, the overwinter accumulation of potentially variable GHG stores remains poorly understood, rendering High Arctic lake emissions both temporally sensitive and difficult to estimate globally come spring. Furthermore, existing studies typically rely heavily on extrapolation, reporting mean lake GHG concentrations from few samples, failing to account for possible GHG heterogeneity. This necessitates a study of sufficient spatial resolution to capture possible heterogeneity and identify its key drivers. Here, we present a robust dataset studying GHG variability in two large, ice-covered lakes in the High Arctic. We collected water samples from 62 sites in May 2023 to measure CO2, CH4 and DO (dissolved oxygen) along with ancillary variables such as conductivity and temperature, and deployed an underwater camera and sonar transducer to examine bottom characteristics (e.g. sediment properties, plant coverage) and observe fish distributions. We utilized this data to hypothesize key spatial drivers of GHG heterogeneity in ice-covered lakes. We observed high variability both within and between each lake for all gases of study. CH4 and CO2 concentrations ranged 0.01-60.6 μmol L-1, and 210-1042 μmol L-1 within our lakes respectively. Sites with high GHG concentrations typically possessed soft sediments and coincided with watershed junctions including stream entrances, exits, and complex geography (e.g. clusters of small islands). Ultimately, we hypothesize that heterogenous GHG concentrations reflect variances in sediment activity driven by watershed inputs, lake morphology, lake volume-to-sediment ratio, and watershed size. Unique to existing literature, this study shows the importance of accounting for heterogeneity when estimating under-ice GHG accumulation in High Artic lakes, and the resolution of our data suggests a fundamental challenge for emissive upscaling lies in fine-scale GHG variability.