Littoral interactions among sediment, water and macrophytes are poorly understood. In particular there is a gap in knowledge concerning the importance of macrophytes as sinks and sources of trace elements. Such knowledge is however central for, amongst others, explaining potential mechanisms behind the community structure of macrophytes and for the development of macrophyte-based indicator values. We studied the interactions between the three matrices (sediment, water and macrophytes) at 19 sampling sites in Storträsket, a 1.7 km2 boreal lake at the land uplift coast of Northern Sweden in summer 2008. The catchment of Storträsket was dominated by coniferous forest of mainly the dwarf-shrub type and open wet mires. The upper sediment layers (0-6 cm) were dominated by fine detritus. Fine detritus dominated also the lower layers (>6 cm but ≤10 cm) at all but four of the studied localities where fine sediments (particle diameter <0.2 mm) dominated. Sediment and water element concentrations were related to element concentrations in the dominating macrophyte species, viz. Nuphar lutea (roots and leaves), Potamogeton natans (leaves) and Sparganium angustifolium (leaves) and to chlorophyll concentrations using uni- and multivariate statistics. We studied 27 major and trace elements. Estimations of abundance and biomass of N. lutea in eight bays was based on the evaluation of high resolution (2 cm) aerial photographs. The total biomass of N. lutea and standardized biomass (biomass per unit of area) differed significantly among bays. Also concentrations in all matrices as well as in chlorophyll showed significant spatial variation in the lake. N. lutea showed for several elements significant partitioning of elements between roots and leaves (e.g. Ca, K, Na, Fe, Pb, Zn). Correlations between element concentrations in sediment/water and in macrophytes were in general weak but significant for amongst others Si in water and leaves of P. natans and Co, Cu and Fe in water and roots of N. lutea. Interpreting correlations of elements between the sediment and macrophytes might in our study be impeded by potential incorporation of lithogenic material in extracellular macrophyte tissue. Our study identified especially N. lutea as a major sink (during vegetation period) and source (during autumn and winter) of several major and trace elements. Interactions between the matrices, chlorophyll concentrations and macrophyte community structure are further discussed as well as the implications of our results for the development of macrophyte-based indicator values.