From 1999 to 2002, the variations in carbon flux due to management practices (shrub removal, thinning) and climate variability were observed in a young ponderosa pine forest originated from clear-cutting and plantation in 1990. These measurements were done at the Blodgett Forest Ameriflux site located in the Sierra Nevada Mountains of California. Thinning in spring 2000 decreased the leaf area index (LAI) by 34% and added 496 g C m−2 of wood and leaf debris at the soil surface. Total ecosystem respiration was not significantly affected by thinning (1261 g C m−2 in 1999 and 1273 g C m−2 in 2000), while canopy photosynthesis decreased by 202 g C m−2. As a result the ecosystem shifted from a net sink of CO2 in 1999 (−201 g C m−2) to a small net source in 2000 (13 g C m−2). Woody and leaf debris resulting from thinning only accounted for maximum 1% and 7% of the total respiration flux, respectively. Thinning did not affect the relative proportion of the different components of respiration to an observable degree. Low soil water availability in summer 2001 and 2002 decreased the proportion of soil respiration to the total respiration. It also imposed limitations on canopy photosynthesis: as a result the ecosystem shifted from a sink to a source of carbon 1 month earlier than in a wetter year (1999). The leaf area index and biomass of the stand increased rapidly after the thinning. The ecosystem was again a sink of carbon in 2001 (−97 g C m−2) and 2002 (−172 g C m−2). The net carbon uptake outside the traditionally-defined growing season can be important in this ecosystem (NEE = −50 g C m−2 in 2000), but interannual variations are significant due to differences in winter temperatures.