Increasing concentrations of the antidepressants amitriptyline and paroxetine were determined recently in marine habitats. However, their impact on marine biota is understudied, despite multiple undesirable effects they have on the environment. An important behavioral aspect that is increasingly measured following exposure to contaminants is the migration of fauna from contaminated areas. Hence, our aim was to better understand the migration pattern of marine meiobenthic fauna, but with a main focus on nematodes, following the exposure to both antidepressants, alone or in mixture. The experiment was carried out in microcosms, which comprised an uncontaminated upper and a lower contaminated compartment, where amitriptyline was added, alone or mixed with paroxetine, at concentrations of 0.4 and 40 µg L−1. The overall abundance of meiobenthic groups decreased significantly following exposure to amitriptyline in both compartments, a pattern augmented by the mixture with paroxetine. The migration of nematodes towards the upper compartments of microcosms was triggered by the level of contamination with antidepressants. As such, the species Terschellingia longicaudata showed no significant change in abundance, suggesting tolerance to both antidepressants. On the other hand, the abundances of nematode taxa Cyatholaimus prinzi, Calomicrolaimus sp., Calomicrolaimus honestus, Neochromadora sp., Chromadorina sp. and Chromadorina minor decreased significantly following the exposure to both antidepressants, even at low concentrations. At the end of the experiment, the dominant migratory nematodes belonged to deposit-feeders and omnivores-carnivores trophic guilds, with tail shapes of e/f types and body-sizes longer than 2 mm. Such functional traits increase their mobility in sediments and the chance to move away from contaminated habitats. Moreover, the sex ratio was imbalanced in the favor of males in contaminated lower compartments with mixtures of the lowest and highest concentrations of amitriptyline and paroxetine, suggesting that these drugs also affect the hormone system. In conclusion, the exposure to the antidepressants amitriptyline and paroxetine triggered important changes within nematode communities, as changes in taxonomic composition were a result of migration and survival of tolerant taxa, but equally acting on the hormone system and leading to unbalanced sex-ratio among the residents.