The isotopic ratio 18O/16O of dissolved O2 in aquatic systems is affected by the preferential biological uptake of 16O (ε). Studies over the past six decades reveal that during incubation experiments, the isotopic effect of microorganism respiration (εorganism) varies in the range of −18‰ to −22‰. In contrast, natural variations in the deep‐ocean O2 concentration and δ18O levels show a considerably weaker effect (~ −10‰). The differences between these observations have been explained to result from either O2 uptake by sediments or organic particles that, due to diffusion‐limited respiration, are expected to weakly fractionate oxygen isotopes, by mixing processes or by weak fractionation at low temperatures. To gain better insight, we studied oxygen demand and δ18O in the deep, cold hypolimnion of Lake Stechlin between 2018 and 2021 as well as in various laboratory incubations. Our incubation results demonstrate an εorganism of about −24‰. Simple model calculations demonstrate a sediment O2 demand isotope effect (εSOD) of about −8.4‰, and a variated water‐column O2 demand isotope effect (εWOD) which is lower than εorganism, ranging from −13.9‰ in 2019 to −23‰ in 2021. Accompanying experiments indicate that the lower magnitude of εWOD may be related to respiration at organic particles lending to a weaker fractionation effect. Thus, variations in εWOD may reflect a changing partitioning of hypolimnion oxygen uptake between suspended particles and their containing microorganisms. Based on own incubation experiments with Daphnia carcasses, we discuss how possible changes of particle rigidity might influence εWOD.