Lake Baikal was studied as a model for elucidating the general pattern of o-phthalic acid diester (PAE) distributions in surface waters with background pollution levels. The influence of factors including congeners, concentrations, sampling points, seasons, years, and potential sources was considered and the environmental risk for various hydrobionts was established. Priority PAEs in Baikal waters are represented by dimethyl phthalate (DMP), diethyl phthalates (DEP), di-n-butyl phthalate (DnBP) and di-(2-ethylhexyl)phthalate (DEHP). Statistically valuable average concentrations and ranges for DMP, DEP, DnBP, and DEHP were 0.02 (0.01–0.02), 0.07 (0.06–0.09), 0.55 (0.47–0.66), and 0.30 (0.26–0.34) µg/L, respectively. The main factors determining PAE concentrations were the year and season of sampling, whereas sampling points were not among the factors influencing PAE levels. The distribution of PAEs in the water body was characterized by (i) an even distribution of minor hydrophilic DMP and DEP congeners in the whole water body, (ii) a maximum concentration of hydrophobic DnBP and DEHP congeners in the upper and near-bottom layers of the water column, and (iii) a low concentration of hydrophobic congeners in the near-shore area. The main PAE source was found to be the atmospheric transfer of polluted air masses, while the supply of PAEs from coastal sources to the pelagic zone was low. The contribution of biogenic sources to the background level of PAEs in the surface waters of Lake Baikal was established. The ecological risk of the background concentration level of PAEs for Lake Baikal biota was estimated. It was found that (i) DMP and DEP congeners do not represent a risk, or represent a very low risk, (ii) the concentration levels of dominant DnBP and DEHP congeners represent a low risk for crustaceans and fishes but (iii) a rather high risk for algae at a DEHP concentration of 0.30 µg/L.