The shallow lakes are important freshwater ecosystems, since they support much of biodiversity and ecosystem services of life on land. Shallow lakes are highly dynamic ecological entities that can exist in several alternative stable states through regime shift caused by a natural or human disturbance that exceeds ecological thresholds for biological communities composition and structure equilibria. The sediment as a reservoir has a key role in the limnological regulation of wetlands linked to the fluxes of nutrients and elements in the biogeochemical interplay with the water and macrophytes. For this reason, the role of sediment in the limnology of the shallow coastal lake of Xuño (NW Iberian Peninsula) was explored by seasonally monitoring the chemical composition of water and sediments, also according to macrophyte species. The shallow depth determines the high availability of light in the bottom and a well-mixed water column maintain the surface of the water–sediment interface oxygenated. The oxic conditions of the bottom implies a top-down regulation of the water column in the Xuño shallow lake that limits the diffusion of phosphorus and trace metals (Fe, Mn, Cu, and Co) to the water, buffering eutrophication or contamination levels by immobilization in the sediments. In fact, the concentration of Hg in the lake water in spring, and also its bioavailability, are high due to its release from the sediment in suboxic conditions. The cover of helophyte species Phragmites Australis and Schoenoplectus Lacustris showed differences in the assimilation of organic monoester and diester phosphorus forms in the sediment. However, the water of the Xuño Lake shows an eutrophic status by the nutrient input associated with the birds populations as indicated by microbiological data.