The lack of correlation between photosynthesis and plant growth under sink-limited conditions is a long-standing puzzle in plant ecophysiology that currently severely compromises our models of vegetation responses to global change. To address this puzzle, we applied data assimilation of a simple carbon (C) balance model to an experiment where sink strength was manipulated by restricting root volume. Our goals were to infer which processes were affected by growth under sink limitation, and to attribute the overall reduction in growth observed in the experiment, to the effects on component processes. Our analysis was able to infer that, in addition to a reduction in photosynthetic rates, sink limitation reduced the rate of utilization of non-structural carbohydrate (NSC), enhanced respiratory losses, modified C allocation and increased foliage turnover. Each of these effects was found to have a significant impact on final plant biomass accumulation. We also found that inclusion of a NSC storage pool was necessary to capture seedling growth over time, particularly for sink limited seedlings. Our approach of applying data assimilation to infer C balance processes in a manipulative experiment enabled us to extract considerable new information from an existing dataset. We suggest this approach could, if used more widely, be an invaluable tool to develop appropriate representations of sink-limited growth in terrestrial biosphere models.