The net ecosystem carbon dioxide (CO2) exchange of invasive plant infestations, such as perennial pepperweed (Lepidium latifolium L.), is not well understood. A characteristic feature of pepperweed's phenological cycle is its small white flowers during secondary inflorescence. Pepperweed flowering causes uniform reflectance over the visible range of the electromagnetic spectrum, thus decreasing the amount of energy absorbed by the canopy and available for photosynthesis. Little is known about how pepperweed flowering and control measures such as mowing affect canopy photosynthesis and autotrophic respiration (FAR) and thus ecosystem respiration. To examine this question, we analyzed CO2 flux measurements made with eddy covariance over a pepperweed infestation in California, covering three growing seasons. Unmowed pepperweed caused the site to be almost CO2 neutral (2007: −28 g C m−2 period−1) or a net source (2009: 129 g C m−2 period−1), mostly because of reduced maximum photosynthetic capacity by 13 (2007) and 17 μmol m−2 s−1 (2009) due to flowering during the plant's prime photosynthetic period. Reference FAR at 10°C was reduced by 2 μmol m−2 s−1 in 2007 and 2009. Mowing during early flowering reversed the attenuating effects of pepperweed flowering, causing the site to act as a net CO2 sink (2008: −174 g C m−2 period−1) mainly due to prolonged photosynthetic CO2 uptake over the plant's early vegetative growth phase. Our results highlight the tight link between pepperweed's prominent key phenological phase and applied control measures, which together exert dominant control over the infestation's CO2 source-sink strength.
 We thank Rodrigo Vargas, Youngryel Ryu (both University of California, Berkeley), and Matthias Peichl (University College Cork) for fruitful discussions during the preparation of the manuscript. We also thank Ted Hehn and Joseph Verfaillie for their dedicated support in conducting the field measurements and servicing the instruments. We thank the Editor, Timothy Griffis, and the two anonymous reviewers for their constructive comments that substantially improved the manuscript. This study was funded by National Science Foundation grant 0628720.