Understanding how environmental conditions and plant functional variation are mutually related is critical to improving our comprehension of plant adaptations. In this context, our knowledge of the interlinks between plant functional, spectral and genetic traits and environmental filters is still very limited, especially for wetland species. To gain new insights on this topic, a multidimensional dataset, centred on the widespread macrophyte species Nuphar lutea, was assembled by collecting data on functional traits (including spectral traits), genetic metrics and environmental determinants from 28 plots spanning north‐central Italy. A strong environmental filter acts on all traits (morphological, biochemical, spectral and the genetic diversity metrics) resulting in significant local control over trait patterns, exemplified by the discrimination value of water electrical conductivity. This is further reinforced by the key contribution of sediment variables in explaining traits variation. Site‐specific environmental conditions were reflected in different patterns of genetic diversity, suggesting a long‐term effect of environmental filters on genotypes as well. High water conductivity – in our study sites indicative of long‐term hydrogeological settings – is linked to more acquisitive behaviour in N. lutea and a progressive reduction in its genetic diversity, while high nutrients availability in sediments promotes higher leaf traits performance. This study better explores how high variability in leaf traits reinforces current genetic and mechanistic knowledge about competitive strategies in the key aquatic plant N. lutea, by testing the effectiveness of a novel integrative approach to assess multiple sources of plant functional variation.