Since the beginning of this century, benthic invertebrates have been used as biotic indicators of water quality. The objective of any lake management plan is both to identify the principal watershed disturbances/practices contributing to a lake problem and to rank their importance as part of a cost-effective abatement strategy. In most cases we see only the end result of the disturbance process without having a sufficient historical data base on either the predisturbance condition or how the biota responded to the type and intensity of disturbance. Without such a data base, the paleolimnological approach is the only way to delineate past lake conditions and the response to disturbance events. Although remains of several faunal groups are preserved in lacustrine sediments, bryozoans, chaoborids, and chironomids show the greatest promise for paleolimnological reconstructions. These groups can be used to make qualitative statements on water quality, but their use in quantitative reconstructions must await construction of calibration models relating subfossil assemblages to known water chemistry and trophic state, and questions on the relationship between producing population and observed subfossil assemblage, postmortem redeposition, differential preservation, and basic ecology are addressed. It is suggested that paleolimnological reconstructions couple detailed land-use histories with multiparameter analyses from dated cores.