Lake pollution has attracted concerns worldwide; especially the excessive accumulation of trace elements (TEs) and rare earth elements (REEs) in bottom sediments can pose a serious threat to ecosystem health. However, there is still a knowledge gap on the level of sediment pollution in lakes isolated from the direct impact of pollution sources, their spatial variability, and also on the factors influencing this state. The aim of this study is to investigate the level and spatial variability of TEs and REEs concentrations, as well as to determine their source and the factors determining their distribution in the bottom sediments of Lake Ostrowite. Lake Ostrowite is the largest and deepest water body located in the Bory Tuholskie National Park (in northern Poland), which completely isolates the lake from the direct impact of pollution sources. The study covered analyses of 32 surface samples of bottom sediments. The concentrations of 24 TEs and 14 REEs were determined using inductively coupled plasma mass spectrometry (ICP‐QQQ‐MS). The assessment of the enrichment of bottom sediments in TEs and REEs employed geochemical background values (GBV) that provided the basis for the calculation of relative concentrations and geochemical indices. The determination of their sources and supply routes was based on the cluster analysis and principal component analysis. The obtained results point to the enrichment of the bottom sediments with TEs and REEs. Relative concentration values of TEs and REEs in reference to geochemical background values were in ranges from 0.01 to 7.31, at an average of 0.99, and from 0.03 to 4.29, averaging 1.76, respectively. The enrichment factor values show moderately severe enrichment of sediments at the study sites. This was primarily determined by the concentrations of Ag (from the TEs group) and Lu (from the REEs group). The metal pollution index values showed an approximate spatial distribution of points in terms of the presence of TEs and REEs. The lowest concentrations of TEs and REEs occurred on the eastern shore of the western basin of Lake Ostrowite. TEs and REEs concentrations in sediments are positively correlated with the content of organic matter and depth and negatively correlated with distance of the sampling point from the river outflow from Lake Ostrowite. On the eastern shore of the western basin, TEs and REEs concentrations are additionally shaped by wind, predominantly from the western direction. With water wave action, organic matter is transported to the central part of the western basin, where it is accumulated. Since the lake is isolated from point and nonpoint pollution sources, relevant from a biogeochemical point of view are dry and wet depositions from the atmosphere as well as aquatic vegetation, shoreline vegetation, forest litter, soil, and groundwater.