The present study aimed to establish potential indicators of fish farming pollution in muddy substrate, by means of meiofauna, and to test whether the effect of the fish farm is more important to determine the meiofauna community than the seasonal environmental conditions. Sampling was performed in spring, after several months of light feeding, and in summer, at high food supply. Samples were collected in three directions at various distances from the floating cages. Harpacticoid copepods and kinorhynchs, whose abundance decreased under the cages, were put forward as indicator taxa. However, harpacticoid copepods were sensitive to fish farm only, while kinorhynchs showed responsiveness to fish farm and to seasonal environmental conditions. Total meiofauna density was dependent on season sensu stricto. The nMDS clearly showed a ‘cage community’ and ‘control community’ in both sampling occasions; therefore it is a good tool for impact assessment.