The response in metal concentrations and isotopic composition to variations in photosynthetic activity of aquatic micro-organisms is crucially important for understanding the environmental controls on metal fluxes and isotope excursions. Here we studied the impacts of two successive diel cycles on physicochemical parameters, Cu and Zn concentrations, and isotopic composition in solution in the presence of mature phototrophic biofilm in a rotating annular bioreactor. The diel cycles induced fluctuations in temperature, pH, and dissolved oxygen concentration following the variation in the photosynthesis activity of the biofilm. Diel variations in metal concentrations were primarily related to the pH variation, with an increase in metal concentration in solution related to a pH decrease. For both metals, δ(66Zn) and δ(65Cu) in solution exhibited complex but reproducible diel cycles. Diel variations in photosynthetic activity led to alternatively positive and negative isotope fractionation, producing the sorption of light Zn (Δ(66Znsorbed-solution) = -0.1 ± 0.06‰) and heavy Cu isotopes (Δ(65Cusorbed-solution) = +0.17 ± 0.06‰) during the day at high pH and the excretion of lighter Zn isotopes (-0.4‰ < Δ(66Znexcreted-biofilm) < +0.14‰) and heavy Cu isotopes (Δ(65Cuexcreted-biofilm) = +0.7 ± 0.3‰) during the night at lower pH. We interpreted Zn and Cu diel cycles as a combination of a desorption of exopolymeric substance-metal complexes and a small active efflux during the night with adsorption and incorporation via an active uptake during the day. The hysteresis of metal concentration in solution over the diel cycle suggested the more important role of uptake compared to desorption and efflux from the biofilm. The phototrophic biofilm presents a non-negligible highly labile metal pool with important potential for contrasting isotopic fractionation at the diel scale.