We present our experiences in monitoring hypoxia and assessing oxygen-related phenomena in aquatic systems, resulting from the EU-FP7 project HYPOX (“In situ monitoring of oxygen depletion in hypoxic ecosystems of coastal and open seas, and land-locked water bodies”, www.hypox.net). For this presentation, we selected approaches and technologies which could be relevant for monitoring fast fluctuations at the pelagic redoxcline, seasonal benthic hypoxia and decadal trends oxycline boundary shifts in the Black Sea. Using novel technologies like e.g., the profiling instrumentation platform GODESS, ARGO floats with oxygen optodes and long-term moorings equipped with ADCP and oxygen optodes, temporal and spatial patterns of water column oxygenation from hours to seasons, and from basin-scale to local-scale patterns were resolved. We present examples from study sites in the Baltic Sea and in the Black Sea. The time series recordings of GODESS and mooring arrays allowed a thorough characterization of oscillating redoxclines in the central Baltic Sea and in the Black Sea off southwestern Crimea as temporally dynamic, three-dimensional systems. For the first time, oxygen sensor equipped ARGO type profiling floats were deployed in the Black Sea and proved to be powerful tools to address seasonal changes in patterns of water column oxygenation on larger spatial scales and emphasize the importance of mesoscale processes for oxygen distribution in the Black Sea basin. A 3-month continuous time series recording of a stand-alone static mooring equipped with optical oxygen sensors, current meters, and turbidity sensors identified summer hypoxia to be a highly dynamic process and provided insights into the controls of hypoxia formation on the north-western Black Sea shelf. Existing multi-decadal time-series monitoring data were used to demonstrate the imprint of climate change and eutrophication on long-term oxygen distributions and, hence, the importance of maintaining long-term commitments to oxygen monitoring programs. Such time series data allow separating out the effects that climatic forcing and eutrophication exert on oxygen depletion i.e., in the Black Sea. Standard CTD measurements in the central Black Sea over the last 90 years reflect the rising of the upper boundary of the suboxic zone in the 1970s and 1980s due to eutrophication, and again in the 1990s and 2000s due to NAO forcing, while eutrophication relaxed. Our comprehensive study within HYPOX was able to address many aspects of hypoxia in aquatic systems and revealed the vital need for dedicated oxygen monitoring at appropriate spatial and temporal scales with appropriate technologies. The variety of hypoxia characteristics and consequences emphasizes also the need for a careful selection of locations and periods of time for oxygen observations in order to adequately address the risk for hypoxia formation and ecosystem response.