Upwelling systems play a key role in the global carbon and nitrogen cycles and are also of local relevance due to their high productivity and fish resources. To capture and understand the high spatial and temporal variability in physical and biogeochemical parameters found in these regions, novel measurement techniques have to be combined in an interdisciplinary manner. Here we use high-resolution glider-based physical–biogeochemical observations in combination with ship-based underwater vision profiler, sensor and bottle data to investigate the drivers of oxygen and nitrate variability across the shelf break off Mauritania in June 2014. Distinct oxygen and nitrate variability shows up in our glider data. High-oxygen and low-nitrate anomalies were clearly related to water mass variability and probably linked to ocean transport. Low-oxygen and high-nitrate patches co-occurred with enhanced turbidity signals close to the seabed, which suggests locally high microbial respiration rates of resuspended organic matter near the sea floor. This interpretation is supported by high particle abundance observed by the underwater vision profiler and enhanced particle-based respiration rate estimates close to the seabed. Discrete in situ measurements of dissolved organic carbon and amino acids suggest the formation of dissolved organic carbon due to particle dissolution near the seabed fueling additional microbial respiration. During June an increase in the oxygen concentration on the shelf break of about 15 µmol kg−1 was observed. These changes go along with meridional circulation changes but cannot be explained by typical water mass property changes. Thus our high-resolution interdisciplinary observations highlight the complex interplay of remote and local physical–biogeochemical drivers of oxygen and nitrate variability off Mauritania, which cannot be captured by classical shipboard observations alone.