Benthic flora can contribute significantly to gross primary production (GPP) of shallow coastal waters where light reaches the sea bottom. We quantified and compared benthic and pelagic GPP along nutrient gradients in time and space in the shallow estuary, Limfjorden, Denmark, based on monitoring data combined with historical information. Limfjorden experienced a shift from a pristine, benthic-dominated clear water regime with high total GPP in the early twentieth century to a eutrophic, plankton-dominated regime still with high total GPP in the 1980s when nutrient loadings peaked. Recent reductions in nutrient loadings reduced pelagic GPP, particularly in spring, but water clarity and benthic GPP did not increase correspondingly, so total GPP declined. The most nutrient-rich basins have remained plankton-dominated, with benthic vegetation constrained to shallow waters. The results support existing evidence that total GPP of shallow coastal areas does not increase systematically with eutrophication. Furthermore, the results suggest that total GPP may decline temporarily during oligotrophication as pelagic GPP declines, while feedback mechanisms delay or prevent restoration to a state with benthic dominance of GPP.