Paleolimnology combines the disciplines of limnology, geology and ecology, but because of challenges that separate investigators from direct knowledge about past lake conditions, the field is multidisciplinary by necessity. As a result, paleolimnology is influenced continuously by advances in many disciplines. As with limnological studies in recent decades, paleolimnology has diverged largely from the ecological and theoretical focuses of early investigators, but recent studies demonstrate the need for more integration of ecological and paleolimnological research. This paper provides a brief overview of recent paleolimnological investigations that have addressed questions related to theoretical ecology, as well as applied lake-management and climate research issues. We examine the use of transfer function models for estimating past water-quality conditions, and important caveats expressed by investigators about limitations in the development and use of such models. Paleolimnological research has contributed new insights about biological, physical and chemical processes in lakes that have been subject to change because of climate drivers and anthropogenic influences. These findings are relevant to predicting how lakes will respond to climate change, and will require new management approaches in the future. As the range of paleolimnological studies expands, there will be greater need for basic limnological research in order for paleolimnological investigators to better understand how sediments reflect lake processes of those regions.