Fish predation has an important role structuring benthic and planktonic assemblages in shallow waters. Habitat complexity may mitigate the effect of fish predation, thus reducing prey–predator encounters and prey capture ability. In this respect, benthic organisms may be less affected by predation than planktonic organisms because macrophytes would increase habitat complexity, thus providing a physical refuge. However, certain small fish may move and live within vegetation, resulting in an increase in prey–predator encounters, and so physical refuges provided by macrophytes would be less effective. To test the effects of small fish on aquatic invertebrates, we performed a field experiment using mesocosms in a Mediterranean salt marsh, using Aphanius iberus as the small fish species (b5 cm) and Ruppia cirrhosa as the dominant macrophyte. Although, A. iberus preys on benthic and planktonic organisms, it has traditionally been described as a benthic species. Hence, a stronger effect on benthos is expected if habitat complexity does not reduce the predation ability of this small fish. We therefore analyzed and compared the strength of the effects of A. iberus on both benthic and planktonic organisms. The fish was found to have stronger effects on planktonic than benthic organisms. The presence of A. iberus was coincident with a decline in the abundance of large water-column invertebrates such as gammarids and jellyfish, and an increase in the abundance of medium-sized plankton. The total biomass of the benthic assemblage increased when A. iberus was present. These results suggest that aquatic invertebrates of Mediterranean salt marshes may use macrophytes as refuge from small fish species