Because they are intensively managed, agricultural ecosystems have a potentially important role to play in near-term strategies to mitigate increases in atmospheric CO2, but real gains have been difficult to demonstrate.  Rye as a cover crop shows considerable promise as a means to increase both GPP and NEE, since it is more resistant to decomposition than other cereals. We found that inclusion of a rye cover crop in a maize/soybean rotation resulted in a substantial increase in GPP during the soybean year, with no discernible impact on GPP of the subsequent maize crop, when compared to a conventional maize/soybean rotation.  Cumulative respiration also increased in the alternative field, though by a lesser amount.  The net effect was that while the conventional field was nearly C-neutral for the biennium with an estimated C loss of 45 g m^-2, the alternative rye/soybean/maize rotation gained approximately 97 g C m^-2, for a net difference between the two systems of 142 g m^-2 for the biennium.  The yield of the subsequent soybean crop was about 15 % lower than the conventional field, apparently due to a delay in ontogeny- the post-rye soybeans were still photosynthesizing at the time of the first killing frost, while the conventional field had already senesced. Contrary to accepted thinking, the rye cover crop did not use more water; in fact cumulative ET for the year was actually a bit less than in the conventional field, and was considerably less for the biennial rotation. This was a consequence of a pronounced effect of the cover crop and its straw residue on albedo, resulting in lower net radiation Water use efficiency was higher in the alternative field for both years.  For the biennium as a whole, the inclusion of the rye cover crop increased water use efficiency by nearly 35%.