Macrophytes are getting increasing attention because of their multiple roles in aquatic ecosystems. However, eutrophication, invasive species and habitat degradation are threatening macrophytes and freshwaters globally. In this context, the use of functional traits (FTs; i.e. specific features measured at species/individual level) can give more quantitatively translatable information than the traditionally adopted taxonomic approach about their ecosystem functions and community dynamics. Here, we incorporate a local patterns approach (hundreds of meters) into trait based macrophytes investigation, focusing on yellow water lily (Nuphar lutea (L.) Sm.). Our aim is to quantify the intra-specific plasticity of a wide set of functionùal traits (including leaf economic spectrum and pigments), integrated with genetic and spectral reflectance data at leaf to canopy scales, linking to ecological patterns. All data were collected from a hyper-eutrophic shallow lake, Chiusi Lake (Central Italy). We found support for trait meso-scale patterns along the main environmental gradients, expressed in terms of water depth, conductivity, and sediment features. A preliminary PCA analysis confirmed what previous studies had shown for aquatic and terrestrial plants, namely that the two main axes of traits variation are related to dimensional traits (leaf weight - LW - and area - LA) on one axis, and Leaf Dry Matter Content (LDMC) and Specific Leaf Area on the other. More specifically, we found that LW and LA, including the contribution of petioles, are positively related to water depth, while leaf pigments content shows a strong relation to water conductivity and sediment phosphorous. This evidence suggests a relevant environmental filtering force on intra-specific responses to abiotic factors and reinforces the key contribution of intraspecific trait variability to shed light on spatial patterns within ecosystems.