In this contribution we challenge the hitherto ruling concept that the total gross primary production (GPP) in shallow coastal areas, i.e. the combined production of micro- and macroscopic plants living in the water and at the bottom, does not change systematically with nutrient enrichment. Based on a large monitoring data set in combination with historical information we have quantified and compared the benthic and the pelagic primary production along nutrient gradients in space and time for the shallow estuary Limfjorden, Denmark. As expected, increases in nutrient load stimulated the pelagic production at the expense of the benthic. Phytoplankton showed a strong positive response to increased nutrient concentrations while benthic primary producers were shaded. The ecosystem thus experienced a regime shift from benthic to pelagic dominance of GPP with increasing load. However, as nutrient load was again reduced, and the ecosystem entered a phase of oligotrophication, pelagic GPP declined gradually while benthic GPP did not increase correspondingly leading to an decline in overall GPP. Instead the ecosystem showed a resistance or time lag against return to a clear water state with benthic dominance.