The unsustainable use of natural resources and overexploitation, which occurs when harvesting exceeds reproduction of wild plant and animal species, continues to be a major threat to biodiversity. 

The ecological footprint analysis compares human demands on nature with the biosphere's ability to regenerate resources and maintain ecosystem services. It does this by assessing the biologically productive land and marine area required to produce the resources consumed and to absorb the corresponding waste, using available technology. Overall biological resources use and waste emission is well above the biological capacity available within Europe, showing that the continent cannot sustainably meet its consumption demands within its own borders. The EU-27 on its own has an ecological footprint of 4.7 global hectares per person, twice the size of its biocapacity. Europe’s high per capita consumption and waste production means that its impact also extends well beyond its borders.

Overfishing is still widespread across the pan-European region with 88 % of Community fish stocks fished down beyond maximum sustainable yields (meaning that less fishing pressure now would allow stocks to recover); 30 % of Community fish stocks are overfished outside safe biological limits that may not allow their recovery.

Non sustainable forest management, intensification measures, the drainage of peatlands and wet forest, fertilization and forest-tree genetic ‘improvement’ have had a particularly negative effect on the biodiversity values of forests. Whilst wood harvesting in the EU is largely sustainable, deadwood (which is a key indicator for forest biodiversity and the conservation value of a forest) remains well below optimal levels from a biodiversity perspective in most European countries.

Intensive agriculture, as currently practiced in Europe, is centred on crop monoculture with minimization of associated species. These systems offer high yields of single products, but depend on high rates of use of fertilizers and pesticides. The maintenance of high productivity over time is unlikely to be sustainable in the face of disturbance, disease, soil erosion and overuse of natural capital (for example water).

Pressures on European water resources have increased in recent decades and in many locations agriculture, energy supply, industry, public water supply and tourism pose a threat to water resources, with demand often exceeding availability. The increase in artificial storage volumes in turns reduces the share of water allocated to natural systems and increases their fragmentation because of damming. Over-abstraction and prolonged periods of low rainfall or drought have frequently reduced river flows, lowered lake and groundwater levels and dried up wetlands. In addition, salt water increasingly intrudes into ‘over-pumped’ aquifers throughout Europe.