This work represents a concerted effort aimed at understanding the microbiological and chemical evolution of a small boreal lake during the diurnal cycle of photosynthesis. We studied diurnal variation of ∼40 dissolved macro- and trace elements, organic carbon and bacterial population dynamics in the surface and bottom water layer of the shallow Vilno Lake in the White Sea basin. Four-days continuous measurements with 6 h sampling steps both at the surface (0.5 m) and on the bottom (4.0 m depth) during no-bloom periods revealed constant concentrations (within ±20–30%) of all major elements (Na, Mg, Si, K, Ca), organic and inorganic carbon and most trace elements (B, V, Cr, Fe, Cu, Ga, As, Rb, Sr, Y, Zr, Sb, Cs, Ba, all REEs, Hf, Pb, Th, U). At the same time, the concentration of some biologically important trace metals (Mo, Mn, Co, Cd) was subjected to variations partially reflecting the change of bacterioplankton concentration. This work enables two types of element behavior to be distinguished during photosynthesis in the water column – constant concentration and sinusoidal variations – depending on their speciation in solution and their affinity to aquatic microorganisms.