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.

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.