This study aimed to investigate how great cormorants and grey herons affect the density and trophic diversity of soil nematodes under breeding colonies located in Stawy Raszyńskie Nature Reserve (central Poland). Soil samples from the colonies were compared to control samples from adjacent areas unaffected by birds. Samples were taken at each site (two colonies and two relevant control sites) to a depth of 20 cm, and the soil cores were split into topsoil (0–10 cm) and subsoil (10–20 cm). A modified Baermann method was used to extract nematodes from the soil. The soil under nests supported more abundant nematode communities, but with a lower trophic diversity compared to the control sites. The cormorants had a greater impact on nematodes than the herons. We found that the external nitrogen input, the higher organic matter content and abundance of ammonifying bacteria, as well as the lower soil pH under the colonies than in the control sites, affected the nematode trophic groups in different ways. Compared to the control sites, there were significantly more bacterivorous nematodes but fewer herbivorous nematodes under the colonies. No predatory nematodes were found under the bird colonies and, in the case of the cormorant colony, no omnivorous nematodes. No significant differences in the abundance of fungivorous nematodes between the impact and the control plots were noticed. The results indicate that allochthonous input under bird colonies promotes microbial activity and the most opportunistic trophic group of nematodes, which may at least temporarily enhance decomposition and mineralisation processes and consequently affect nutrient cycling in the wetland soil.