Most of the research examining changes in aquatic biota relative to increasing acidity has concentrated on pelagic components. The possible influence of littoral-pelagic interactions on observed relationships has largely been ignored, and thus interpretation of pelagic biotic data unfortunately often is taken out of context of the whole ecosystem. While littoral and benthic communities are major contributors to the autotrophic production of small lakes in general, it is likely that their share assumes greater importance in acidic lakes where phytoplankton are often severely nutrient-limited. The availability of nutrients in the pelagic zone of acidic lakes may be regulated by littoral and benthic processes. Available data suggest that while the structure of littoral and benthic autotrophic communities has a direct influence on benthic invertebrates, it exerts an indirect control on zooplankton and fish principally through the quality and quantity of habitat and food resources. Future investigations of biota in acidic soft-water lakes should concentrate on quantifying such littoral-pelagic linkages.