Synthetic surfactants in cleaners and detergents commonly contaminate freshwater systems, therefore use of low-toxicity alternatives is becoming increasingly important. Alkyl polyglucosides (APGs) derived from natural products are less toxic than synthetic surfactants, and degrade rapidly reducing chemical exposure time. However, single species toxicity tests showed APGs have toxic effects on aquatic primary producers and zooplankton, and that species demonstrate different sensitivities to APGs. Furthermore, species unaffected by APGs directly may be indirectly affected by removal of a food source or changes in predator densities, thereby changing plankton community structure. To determine the effects of APGs on plankton communities under environmental conditions, floating mesocosms were deployed in a shallow pond in southeast Georgia, USA and dosed with 0, 0.01, 2.5, 5, or 10mgL-1 APG. Zooplankton community composition and abundance, phytoplankton abundance (as chlorophyll a), and water column dissolved oxygen concentration were determined weekly for 1month. Zooplankton abundance decreased primarily due to loss of copepods, and community composition shifted toward small-bodied cladocerans (Bosmina sp.), and chlorophyll a concentrations declined by up to 81% following exposure to APG concentrations of 2.5mgL-1 or greater. Concentrations of dissolved oxygen never dropped below 5.70mgL-1, but the observed declines of~2mgL-1 could become stressful during periods of high water temperatures. Nevertheless, the APG-induced shift from copepod to cladoceran dominated communities and decrease in autochthonous carbon availability has important implications for food availability and quality to higher trophic levels such as planktivorous fishes.