The eddy-covariance method was used to measure net ecosystem productivity over three adjacent fields from 2009 to 2011: two annual cropping systems (oat-canola-oat and hay-oat-fallow) recently converted from perennial cropping, and a perennial hay/pasture. We compared the management practises, determined the net carbon budget, and examined the effects of inter-annual variability. Carbon accumulation began earlier in the spring and continued later in the fall at the perennial site, compared with the annual crop sites, due to a longer growing season and continual plant cover. Cumulative cropping season net ecosystem productivity at the perennial site ranged from 40 to 240 g C m^(-2) because of variable weather. Including harvest removals and manure additions, the perennial site gained 120 g carbon m^(-2) and the annual sites lost 240 and 415 g carbon m^(-2), respectively, over the 30-month period. This indicates that the annual cropping systems would decrease soil carbon at this location.