High spatial resolution diatom and loss-on-ignition analyses were carried out on the surface sediments of a shallow, medium-sized lake in north-eastern Lithuania to examine the degree of spatial heterogeneity of diatom assemblages in the lake, as well as the influence of water depth on diatom compositions. The compositional properties of sediments and diatom assemblages show a strong relationship with water depth; some less prominent changes were attributed to the tributary catchment. Diatom assemblage compositions are rather homogenous throughout the lake (Morisita-Horn similarity indices make >0.9 in most locations of the lake, in relation to others), especially in its deeper parts. Our case shows that the most representative point does not lie in the centre of the lake, as it is assumed in most of fossil studies. Studies of spatial heterogeneity of modern diatoms can facilitate site selection and fossil diatom data interpretation.