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Subfossil chironomid (Diptera, Chironomidae) remains are often used as indicators of lake level changes in palaeolimnological studies. However, their usefulness as a water depth proxy can vary between the sites, depending on the lake morphology, mode of taphonomic processes or amplitude of past water level fluctuations, among other factors. In this study, we have examined the distribution of subfossil chironomids in the shallow Lake Spore (northern Poland) to assess the influence of water depth on the fauna. Our aim was to evaluate the site-specific utility of subfossil chironomids for lake level reconstruction at Lake Spore. The subfossil chironomid assemblages in Lake Spore have heterogeneous distribution, suggesting they are predominately composed of remains deposited close to the sampling location. A strong relationship between the water depth and the chironomids is marked by the 25.12% variance explained by water depth in the taxonomic data. Moreover, according to generalized linear models (GLMs) out of 44 dominant taxa, 12 have significant relationships with water depth. However, the sensitivity of our chironomid fauna to water depth changes is not continuous along the entire depth gradient. The most abrupt assemblage change occurs at 2.6–3.7 m water depth, in proximity to the depth where macrophytes become less dense and finally disappear. We conclude that, despite these strong chironomid-water depth relationships, only major water level fluctuations can be satisfactorily reconstructed due to the limited turnover rates of the fauna along a depth gradient and relatively small amplitude of the lake level variations characteristic for East-Central Europe.