Some studies have reported that spring warming and earlier snowmelt leads to increased CO2 sequestration in Arctic terrestrial ecosystems. We measured tundra-atmosphere CO2 exchange via eddy covariance at two low Arctic sites (mixed upland tundra and sedge fen) in central Canada over multiple snow-free periods to assess this hypothesis. Both sites were net sinks for atmospheric CO2 in all years (2004–2010), but with high interannual variability. Despite a large range in snowmelt date (30 days), we did not find a statistically significant correlation between seasonal accumulated net ecosystem production (NEP) and snowmelt for either site. Although many factors can influence seasonal total NEP, our analysis shows that annual variations in photosynthetic capacity, likely driven by changes in leaf area, is a dominating control at these Arctic sites. At the upland tundra site, protection of overwintering buds by a longer duration of deep snow appears to be linked to greater photosynthetic capacity and NEP. Whereas at the fen site, sedge growth benefits from earlier snowmelt resulting in a strong correlation with early season NEP and an increase in total study period NEP with increasing growing degree days. These results highlight the complexity of interannual variation in ecosystem CO2 exchange in Arctic tundra and suggest that snowmelt date alone cannot predict seasonal, or annual, NEP.