In Slovenia, alluvial aquifers present 60 % of the drinking water sources, and karst-fractured aquifers present 40 %. Due to populated areas and intensive agricultural production, alluvial aquifers are exposed to greater risks of pollution with nitrates.

Organic matter in soil is an important indicator of the quality of soil. In general, soil in Slovenia is well supplied with organic matter; this is evident from soil map data, which indicate that 86.2% of agricultural land contains more than 2% of organic matter, and 30.9% of land contains more than 4%. The results of laboratory analyses of soil samples taken in 2005 present a similar picture: 88.6% of samples contained more than 2% of organic matter and 37.3% of samples contained more than 4% or organic matter.