The process installations and storage reservoirs of a petroleum refinery have leaks of petroleum products (PP) that pollute soil, underground waters, and eventually nearest water objects, by worsening their hygienic state. Environmental and economic assessments of the Angara River water protection system that is in operation at the petroleum refinery OAO "Angara Petroleum Company", which comprises well clusters, a gravel-filled trench, and a drainage system, have shown the high values of preventable relative natural and economic damages and other economic indicators. At the same time, comparison of the amount of PPs accumulated at the industrial site with their annual withdrawal has demonstrated a need for further development of a river protection system. Therefore the environmental protection system efficacy evaluated by the quality of goal attainment and by means of a matrix of algorithmized statements was 60% or 5 of 20 scores, which shows the necessity of special measures to protect Angara River waters. The elaboration and implementation of these measures associated with considerable expenditures make it possible not only to increase the environmental efficiency of water protection of the Angara River, but also to do the hygienic quality of water use in its related localities.