The exchanges of carbon dioxide (CO2), water vapor, and energy were measured nearly continuously since 1996 over a mixed mature transition forest at the Borden Forest Research Station, in southern Ontario, Canada. Borden Forest, one of the longest running flux towers in North America, is located in the temperate–boreal ecotone. This transitional region, which includes species close to the limits of their environmental range, may be particularly susceptible to changes in forest composition as a result of climate change. Here we analyze net CO2 exchange, measured using the eddy covariance method, and concurrent meteorological variables. The forest was found to be a low-to-moderate CO2 sink, with uptake of 177 ± 28 gC m−2 yr−1 (mean ± standard error). In two of the years, however, the forest was a weak CO2 source (i.e., 1996: −36 gC m−2 yr−1 and 2001: −35 gC m−2 yr−1), demonstrating that the forest can switch between source and sink. Over the 17 years of measurement, annual net ecosystem productivity (NEP) increased by 15.7 gC m−2 yr−1 yr−1, due to a decline in ecosystem respiration of 4.2 gC m−2 yr−1 yr−1 and an increase in gross ecosystem productivity of 11.6 gC m−2 yr−1 yr−1. There were notable long-term indications of climatic warming: annual air temperature rose by 0.09 °C yr−1, while soil temperature increased by 0.08 °C yr−1. Photosynthetically active radiation and soil temperature were found to be the dominant environmental drivers of interannual variations and long-term trends in NEP; on seasonal or monthly time-scales, air temperature and precipitation also influenced CO2 uptake. NEP is positively correlated with the length of the net carbon uptake period, which varied from 111 to 164 days. The large interannual variations in CO2 flux in this dataset demonstrate the need for long time series of CO2, water vapor, and energy fluxes, together with meteorological measurements; such measurements show long-term trends, which can be used to understand and predict future changes in forest-atmosphere exchanges in response to anticipated changes in climate.