Combining existing traditions of rice and of fish in an integrated rice−fish (IRF) culture is a promising strategy for sustainably increasing land productivity and diminishing the need for external inputs in smallholder agriculture of Amazonia. This study evaluates the potential of IRF for weed control in irrigated rice production. It was conducted from August 18 to December 5, 2008 in the Maranhão lowlands in the eastern periphery of Amazonia. We compared weed communities in four 3-year-old IRF and four adjacent ‘conventional’ irrigated rice (CIR) fields at 20 and 40 days after transplanting (DAT), at the mid-vegetative stage and at the onset of flowering, which served as an indicator of potential grain yield. Rice–fish fields contained differing mixtures of herbivore and omnivore fish species totaling 4000 fish per ha or 1.7 fish per m3. Total weed density was reduced in the IRF system, particularly early in the season, the most critical stage for rice development. The integration of fish into irrigated rice cultivation affected weed species composition, with fish-weeding preferentially reducing monocotyledonous Cyperaceae, one of the more aggressive and problematic weed families in this region. Monocot weed density was negatively correlated with rice aboveground biomass at 40 DAT rice. Although floristic similarity between IRF and CIR fields was low, the impacts of IRF on weed species diversity and weed species richness were not significant. Thus, IRF was not associated with a simplification of the weed community. We conclude that fish-weeding may substitute for manual or chemical weeding in irrigated rice agriculture, an important consideration for resource-poor smallholder agriculture in environmentally sensitive riverine or delta areas of eastern Amazonia.