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Anthropogenic nitrogen (N)-loading has decreased significantly in the Baltic Sea Transition Zone over the past two decades. We show that the vertical distribution of primary production (PP) changed as a function of landbased N-loading using 1385 water column photosynthesis estimates, in which photosynthetic parameters were determined both in the surface water layer and in the pycnocline-bottom layer (PBL) at six stations near the Danish coast between 1998 and 2012. Total annual PP and surface layer PP (SPP) correlate positively with landbased N-loading from Denmark (p , 0.003). The percentage of annual PP occurring in the PBL (denoted as deep primary production, DPP) varied annually between 6% and 30% (mean 5 17%). The absolute magnitude of the DPP, as well as its relative proportion of total water column PP, correlates negatively with N-loading (p , 0.009 and p , 0.0003, respectively). Thus, SPP decreases in response to decreased N-loading, while DPP increases. Land-based N-loadings also correlate positively with the light attenuation coefficient (R 2 5 0.39, p , 0.05), which may in part explain the response in DPP to changes in N-loading. DPP occurs in active phytoplankton communities acclimated and/or adapted to low light and producing oxygen in the PBL water.