Light reduction in the water column and enhanced organic matter (OM) load into the sediments are two main consequences of eutrophication in marine coastal areas. This study addresses the combined effects of light, OM, and clonal traits in the seagrass Zostera noltii. Large Z. noltii plants were grown in sand with or without the addition of OM and under two light levels (high light and low light). Whereas some complete plant replicates were grown under homogeneous light and/or OM conditions, other replicates were grown under contrasting light and/or OM levels between the apical and the distal parts of the same plant. The three-way factorial design (light, OM load, and apex position) allowed us to determine the harmful effect of light reduction and OM enrichment on the growth, photosynthetic performance, and biochemical composition of Z. noltii. The addition of OM to the sediment promoted a decrease, or even an inhibition, in net plant growth regardless of the light level when the whole plants were grown under homogeneous light conditions. However, the results differed when plants were grown under contrasting light and/or OM conditions between apical and distal parts. In this case, the harmful effect of OM load was alleviated when apical parts were grown under high light conditions. OM loads also negatively affected the photosynthetic performance, evaluated as leaf fluorescence. The results indicate the importance of clonal traits in the response of Z. noltii growth to light conditions and OM enrichment.