Coastal hypoxia is intensifying worldwide, threatening biodiversity, fisheries, and essential ecosystem services. Through intensive on-going research, the IOW group „Shore-to-Basin (S2B)“ made observations revealing a previously underrecognized phenomenon in the shallow Baltic Sea: hypoxic waves, rapid bottom-water oxygen declines (100 µmol L⁻¹ decay within hours). These short-lived events are largely missed by routine monitoring and absent from most models, yet they may strongly perturb sediment redox conditions, nutrient cycling, and greenhouse gas emissions. HypoWaves combines high-resolution oxygen and turbulence observations, process-based incubation and isotope-tracer experiments with coupled hydrodynamic–biogeochemical modeling (GOTM with a benthic compartment) to (i) identify the physical and biogeochemical triggers of hypoxic waves, (ii) quantify their impacts on nitrogen cycling, phosphorus mobilization, and on nitrous oxide (N₂O) production, and (iii) develop indicators and parameterizations to predict episodic hypoxia under future climate scenarios. Within the broader Baltic Challenge, a focused 3-year PhD project within Objective 2 will resolve how repeated short-term oxygen depletion shifts of nitrate (NO₃^-) reduction pathways and N₂O formation. Together, the project will establish a mechanistic and predictive framework to understand episodic oxygen loss and its biogeochemical consequences in the Baltic Sea, with broad applicability to shallow coastal systems worldwide.