Over recent decades, a great number of pit lakes have been formed, as a result of sand and gravel quarrying in river floodplains that are often also heavily exploited for agriculture. These lakes can act as nutrient filters and regulate the nitrogen pollution resulting from agricultural fertiliser use. In this paper we report the main outcomes of a study of the major nitrogen pathways in five pit lakes of differing trophic status, located along a lowland stretch of the Po river (Northern Italy). Benthic nitrogen fluxes and denitrification rates were determined in the hypolimnion and denitrification and reactive nitrogen assimilation by microphytobenthos in the littoral zone. We tested the hypothesis that lake depth and trophic status can impair denitrification and/or reactive nitrogen assimilation, compromising the function of the lakes as nutrient filters. In the studied lakes, denitrification and reactive nitrogen assimilation by primary producer communities accounted for substantial nitrogen removal rates, which were among the highest reported in the literature. Benthic nitrogen fluxes and denitrification varied between and within lakes, with depth. The littoral zone and surface waters also supported primary production, favouring nitrogen assimilation and temporal retention in the primary producer biomass. In all lakes, denitrification rates decreased from littoral to hypolimnetic sites. Denitrification rates and net nitrogen assimilation also diminished from oligotrophic to eutrophic conditions. To some extent, in eutrophic lakes there was a transfer of primary production from the benthos to the water column and the benthic system became heterotrophic, reducing the capacity for net nitrogen removal. Overall these results highlight that floodplain pit lakes can provide ecosystem services formerly supplied by natural wetlands. An important factor for management is the development of extensive littoral and shallow water zones, which are critical for maximising the nitrogen removal.