To provide insights into the long-term evolution of aquatic ecosystems without human interference, we here evaluate a decadal- to centennial-scale-resolution diatom record spanning about 12 ka of the Holsteinian interglacial (Marine Isotope Stage 11c). Using a partially varved sediment core from the Dethlingen palaeolake (northern Germany), which has previously been studied for palynological and microfacies signals, we document the co-evolution of the aquatic and surrounding terrestrial environment. The diatom record is dominated by the genera Stephanodiscus, Aulacoseira, Ulnaria and Fragilaria. Based on the diatom assemblages and physical sediment properties, the evolution of the Dethlingen palaeolake can be subdivided into three major phases. During the oldest phase (lasting ∼1900 varve years), the lake was ∼10–15 m deep and characterized by anoxic bottom-water conditions and a high nutrient content. The following ∼5600 years exhibited water depths >20 m, maximum diatom and Pediastrum productivity, and a peak in allochtonous nutrient input. During this phase, water-column mixing became more vigorous, resulting in a breakdown of anoxia. The youngest lake phase (∼4000–5000 years) was characterized by decreasing water depth, turbulent water conditions and decreased nutrient loading. Based on our palaeolimnological data, we conclude that the evolution of the Dethlingen palaeolake during the Holsteinian interglacial responded closely to (i) changes within the catchment area (as documented by vegetation and sedimentation) related to the transition from closed forests growing on nutrient-rich soils (mesocratic forest phase) to open forests developing on poor soils (oligocratic forest phase), and (ii) short-term climate variability as reflected in centennial-scale climate perturbations.