Wetland ecosystems are known to mitigate high nutrient loadings and thus can improve water quality and prevent potential biodiversity loss caused by eutrophication. Plant traits affect wetland processes directly through effects on accumulation or metabolization of substances, and indirectly by affecting microbial transformation processes in the soil. Understanding the causes and consequences of intraspecific variation in plant functional traits and associated ecosystem processes can aid applied ecological approaches such as wetland restoration and construction. Here we investigated molecular variation and phenotypic variation in response to three levels of nitrogen availability for a regional set of populations of the common wetland plant Juncus effusus. We asked whether trait expression reveals signatures of adaptive differentiation by comparing genetic differentiation in quantitative traits and neutral molecular markers (QST-FST comparisons) and relating trait variation to soil conditions of the plant's origin. Molecular analyses showed that samples clustered into three very distinct genetic lineages with strong population differentiation within and among lineages. Differentiation for quantitative traits was substantial but did not exceed neutral expectations when compared across treatments or for each treatment and lineage separately. However, variation in trait expression could be explained by local soil environmental conditions of sample origin, e.g. for aboveground carbon-to-nitrogen (C:N) ratios, suggesting adaptive differentiation to contribute to trait expression even at regional level.