In Slovenia, 98.7% of surface water bodies are in good chemical condition. The two water bodies are in poor chemical condition due to the excess of metals. In general, Slovenian surface waters are not loaded with priority substances in the water, but they are loaded with too high concentrations of mercury and brominated diphenylethers in fish. These are ubiquitous pollutants that are excessively present in biota both in Slovenia and in Europe.

Good or better ecological status is estimated for 49% of surface water bodies. The main reasons for the moderate or poorer ecological status of surface waters are hydromorphological change and general degradation, which are evaluated on the basis of the status of benthic invertebrate and fish communities. Compared to the previous assessment period, good ecological status is achieved by 9% fewer water bodies.