Nutrient over-enrichment remains the key environmental challenge for lakes and reservoirs in Slovenia. For the assessment period 2014–2019, only 4 of the 11 lake water bodies achieved good or high ecological status. Recent annual data indicate no signs of improvement, and in some lakes total phosphorus concentrations are even rising. The main pressures are linked to human activities, especially inappropriate discharge of municipal wastewater, intensive agriculture in the catchments, and fisheries.

The values ​​of the parameters used to monitor the load of rivers with organic substances have decreased significantly since 1996. The observed decrease in organic load corresponds to the increase in the proportion of the population whose wastewater is treated in municipal and joint wastewater treatment plants. The load of rivers with nutrients varies significantly between river basins. The average nitrate values ​​in all river basins of the Danube river basin are higher than in the Soča and Adriatic river basins and above the values of the natural background.

The value of agricultural output in Slovenia fluctuates in the period 1995–2024, which can be a consequence of fluctuation of changes in prices of agricultural products, changes in the volume of agricultural production or combination of both. In the recent period, the key factors have been large fluctuations in the physical volume (and consequently the value) of agricultural production, especially in crop production. In recent years, there have been intense fluctuations in crop prices and prices of agricultural inputs.

In Slovenia, the majority of food is estimated to be imported. Before 2004, less than half of all available food came from abroad, but both food imports and exports increased significantly after Slovenia’s accession to the EU. The share of imported food has since continued to grow, and after 2020, less than one-fifth of the available food was of domestic origin. Most of the food Slovenia imports comes from European Union Member States, with about 60% originating from neighbouring countries (Austria, Croatia, Italy, and Hungary).

In Slovenia, the breeding of indigenous domestic animals is becoming less attractive, and out of 15 indigenous breed 14 are endangered. The Carniolan honeybee being the only exception. Thirteen out of 14 traditional breeds are also endangered. The share of introduced animal breeds and crossbreeds with introduced breeds has been increasing. The breeds and races where the adaptation to natural conditions is the strongest are the most successful with defining the introduced breeds.