We summarized studies on the impacts and scale effects of negative (competition, predation, parasitism, herbivory) and positive (mutualism, commensalism, indirect facilitation) species interactions in freshwater benthic habitats since ∼1986 and focused on organisms with mainly or entirely aquatic life cycles. Benthologists publishing in J-NABS have contributed robustly to our overall knowledge of predation and herbivory but less so of other species interactions. Predators can limit the abundance of benthic prey and affect prey size or age structure, behavior, and morphology, and these effects can be transmitted through food webs and ecosystems. Herbivores can limit biomass of benthic algae, alter physiognomy, species composition and diversity, and stoichiometry, and exert strong indirect effects within food webs and nutrient cycles. Parasites can alter host behavior or morphology, but few studies have shown that lethal/sublethal effects of parasites on their hosts have population- or community-scale consequences. Fishes and macroinvertebrates occasionally experience competition, but the effect of competition on demographies and assemblages appears restricted to local scales, perhaps because competition can be modulated by many biotic (bioenergetic efficiency, parasitism, predation) and abiotic (floods, drought, resource distribution) factors. Positive interactions have been the least studied species interaction by benthologists, but interest is growing. Future study of population-scale positive interactions and nontraditional interactions at larger scales (e.g., riparian effects on benthic habitat stabilization, cross-system recruitment of different life stages) will improve our understanding of freshwater benthic ecosystems and their conservation. We urge benthologists to explore how populations evolve in response to biotic interactions embedded in benthic communities and to assess how these responses might redefine trophic and community structure and their emergent properties.