While light availability plays a critical role in seagrass growth and distribution, there is limited understanding of how changes in light exposure impact belowground processes. We investigated the effect of prolonged and fluctuating reductions in light on root growth and exudation by three colonizing seagrasses: Cymodocea serrulata, Halophila ovalis, and Halodule uninervis. Seagrasses were grown in mesocosms under continuous full light (control), under continuous light reduction (medium or low), or under fluctuating light (10 d of low and 4 d of high light, repeated three times). Plants were harvested (1) 6 weeks after light treatments (impact), and (2) after an additional 4 weeks of continuous full light (recovery). Root exudates were collected from trap solutions and measured for dissolved organic carbon (DOC), total dissolved nitrogen (TDN), and dissolved organic matter (DOM) excitation/emission fluorescence spectroscopy. Root biomass decreased in all shading treatments. The most notable impact of light treatment was an increase in root exudation of DOC, protein-like DOM and humic-like DOM under fluctuating light for all species. After 4 weeks of recovery, exudation of DOC, and protein-like DOM observed under fluctuating light returned to the control light levels. However exudation of DOC and protein-like DOM by H. ovalis grown in continuous low light remained greater than the control, likely due to root death. This study suggests the belowground environment of seagrasses is sensitive to light reduction. Monitoring changes in root exudation of seagrasses can provide an effective and rapid method to assess light stress and short-term recovery of seagrasses.