Contribution of boulder reef habitats to oxygen dynamics of a shallow estuary

We assessed the importance of boulder reefs to the oxygen dynamics of a shallow estuary during two growing seasons in 2017 and 2018. Using open-system diel oxygen measurements and benthic and pelagic incubations, we evaluated the relative contribution of pelagic and benthic habitats to the ecosystem metabolism along a depth gradient in two areas, with (Reef) and without (Bare) boulder reefs in the Limfjorden, Denmark. System integrated areal rates of gross primary production (GPP) and ecosystem respiration (ER) both increased with depth in both areas. Benthic contribution to system GPP and ER was highest at shallow depth where it represented 47 and 53% respectively. However, with increasing depth pelagic processes dominated GPP and ER (98 and 94%) even in the Reef area. Although the Reef area had higher biomass of auto- and heterotrophic organisms (macroalgae and macrofauna), benthic GPP was at similar level in both areas, due to a significant contribution from micro-phytobenthic organisms. The Reef area had lower sediment pools of organic matter, nitrogen and phosphorous and was slightly more oxygenated compared to the nearby Bare area. Extreme temperatures and higher levels of nutrients in 2018 caused a marked increase in benthic ER rates resulting in net heterotrophy (NEM = GPP − ER)  0) in 2017. Under current eutrophic conditions, boulder reefs do not contribute positively to the oxygen dynamics in the estuary. Reoccurring blooms of phytoplankton with high organic matter decomposition combined with high temperatures and dominance of fauna stimulate depletion of oxygen around the reefs. Significant improvements in water clarity are needed to regrow perennial macroalgae and induce net autotrophy. Under current turbid conditions, it is only recommended to establish boulder reefs in shallow (