Large omnivorous predators may play particularly important roles determining the structure of communities because of their broad diets and simultaneous effects on multiple trophic levels. From June 2001 to June 2002 we quantified community structure and ecosystem attributes of six newly establishing freshwater ponds (660 m2 each) after populations of omnivorous crayfish (Orconectes virilis) were introduced to three of the ponds. Crayfish preyed heavily on fish eggs in this experiment, which reduced recruitment of young-of-year fish. This effect indirectly enhanced zooplankton biomass in crayfish ponds. Phytoplankton abundance exhibited a more complex pattern and was probably influenced by non-trophic (e.g., bioturbation) effects of crayfish. Peak dissolved oxygen levels were lower in the crayfish ponds indicating that they had lower primary production: respiration ratios. Metaphytic algae were strongly affected by crayfish presence; filamentous greens quickly disappeared and the blue-green Gleotrichia (a less preferred food item) eventually dominated the composition in crayfish ponds. Chara vulgaris and vascular macrophytes established 34% cover in control ponds by June 2002, but were not able to establish in crayfish ponds. Two important periphyton herbivores (tadpoles and gastropods) were absent or significantly reduced in the crayfish ponds, but periphyton differences were temporally variable and not easily explained by a simple trophic cascade (i.e., crayfish-snails and tadpoles-periphyton). Our results indicate that crayfish can have dramatic direct and indirect impacts on littoral pond communities via feeding links with multiple trophic levels (i.e., fish, invertebrates, and plants) and non-trophic activities (bioturbation). Although the effects of omnivorous crayfish on littoral communities can be large, their complex effects do not fit neatly into current theories about trophic interactions or freshwater community structure.