The decline of dissolved oxygen in the oceans could be detrimental to marine life and biogeochemical cycles. However, predicting future oxygen availability with models that mainly focus on temporal and spatial large-scale mean values could lead to incorrect predictions. Marine ecosystems are strongly influenced by short temporal- and small spatial-scale oxygen fluctuations. Large-scale modelling neglects fluctuations, which include the pervasive occurrence of high oxygen supersaturation on a daily time scale in productive ecosystems such as coral reefs, seagrass meadows and mangrove forests and the spatial heterogeneity in oxygen availability at microclimatic scales. In these temporal and spatial micro-environments, oxygen fluctuations control biogeochemical cycles and alter community responses to, for example, heat stress and hypoxia. Robust projections on the impact of predicted ocean and coastal deoxygenation require a better understanding of the dynamics of the dissolved oxygen coupled with scaled-down projections of oxygen fluctuations at small relevant scales for marine biogeochemical processes and communities. Overall, the study of the true oxygen dynamics in marine productive habitats can provide crucial insights into the feedback mechanisms between climate change and marine ecosystems and can help to develop effective management and conservation strategies.