The relative abundances of nitrifying, denitrifying and anammox prokaryotes in sediments of three hypernutrified estuarine tidal flats of Laizhou Bay, Bohai Sea, China were investigated. Quantitative PCR estimates indicated that in most cases archaeal (AOA) amoA genes were more abundant than bacterial (AOB) amoA genes, and ratio of AOA/AOB was correlated with pH, Cd and Cu. Of the denitrifiers, nirK-type outnumbered nirS-type, with nosZ-type being the lowest. Variation of the ratio between nirK and nirS abundance depends on pH, nitrite, nitrate and Cd. The combination of (nirS+nirK-nosZ), an indicator of genetic potentials for N2O emission, was only related to the temperature. Anammox bacterial 16S rRNA gene abundances were correlated with salinity, pH, nitrite, and Cu. In contrast, the contribution of anammox to N2 production, by using anammox bacterial 16S rRNA/nosZ ratio as a proxy, was correlated to temperature, ammonium and dissolved oxygen in the overlying water, ratio of organic carbon to nitrogen and arsenic in sediments. Our study stresses that abundances of N-cycling functional groups respond differently to variations of environmental conditions, and multiple factors including heavy metals with relatively low concentrations may play a role in shaping nitrogen cycling processes in these estuarine tidal flats.