1. Palaeolimnology and contemporary ecology are complementary disciplines but are rarely combined. By reviewing the literature and using a case study, we show how linking the timescales of these approaches affords a powerful means of understanding ecological change in shallow lakes.

2. Recently, palaeolimnology has largely been pre‐occupied with developing transfer functions which use surface sediment‐lake environment datasets to reconstruct a single environmental variable. Such models ignore complex controls over biological structure and can be prone to considerable error in prediction. Furthermore, by reducing species assemblage data to a series of numbers, transfer functions neglect valuable ecological information on species’ seasonality, habitat structure and food web interactions. These elements can be readily extracted from palaeolimnological data with the interpretive assistance of contemporary experiments and surveys. For example, for one shallow lake, we show how it is possible to infer long‐term seasonality change from plant macrofossil and fossil diatom data with the assistance of seasonal datasets on macrophyte and algal dynamics.

3. On the other hand, theories on shallow lake functioning have generally been developed from short‐term (<1–15 years) studies as opposed to palaeo‐data that cover the actual timescales (decades–centuries) of shallow lake response to stressors such as eutrophication and climate change. Palaeolimnological techniques can track long‐term dynamics in lakes whilst smoothing out short‐term variability and thus provide a unique and important means of not only developing ecological theories, but of testing them.

4. By combining contemporary ecology and palaeolimnology, it should be possible to gain a fuller understanding of changing ecological patterns and processes in shallow lakes on multiple timescales.