Modern approaches to environmental regulation require that regional background concentrations of pollutants in environmental objects are set to serve as the basis for an objective assessment of the geoecological situation at a certain spatial level using monitoring data. The determination of the regional background levels of pollutants in sediments is particularly relevant due to the lack of matching sanitary standards for their permissible concentrations in the Russian Federation. Petroleum hydrocarbons, being structural components of natural organic matter, enter water bodies also from anthropogenic sources. Their accumulation in sediments leads to secondary water pollution and alteration of the structural and functional characteristics of the aquatic ecosystems. The natural component of petroleum hydrocarbons must be taken into account when determining their background levels in sediments. Based on representative material and using a statistical approach, the background concentrations of petroleum hydrocarbons in sediments of rivers, storage reservoirs and lakes of the Republic of Tatarstan were calculated. The structure of the variability in the content of petroleum hydrocarbons in the sediments is represented by the ratio of three factors: the hydrological conditions, organic matter content, and the particle size distribution (the pelite fraction content) of the sediments. The baseline value of the background concentration of petroleum hydrocarbons in sediments of water bodies in the Republic of Tatarstan is the median of the series, and its upper quartile serves as the criterion telling whether the value is within the regional background. Minimal background concentrations of petroleum hydrocarbons – 45 to 180 mg/kg (the upper limit of 100‒475 mg/kg) – are typically found in the sediments of rivers and storage reservoirs. In lake sediments, where the proportion of organic matter and clay particles is higher due to hydrological and production characteristics, the background content of petroleum hydrocarbons is estimated to be much higher – 90‒320 mg/kg, and the upper limits of the background content are 195‒510 mg/kg.