The first freshwater science-based targets focus on two key issues: water use, specifically withdrawals from surface water bodies and groundwater, and freshwater pollution resulting from nitrogen and phosphorus.

These pressures are the first to be addressed by freshwater science-based targets because of their relevance to the majority of companies (freshwater use), their significance in specific sectors and environmental issues (freshwater pollution, and are together two of the key pressures that are driving the loss of nature in ecosystems around the world.

Many pressures from human activity affect the functioning of healthy freshwater systems. In terms of water quantity, the current version of the Step 3 tasks focuses on water withdrawals—the extraction of water from surface sources (rivers and lakes) and groundwater sources (aquifers).

Water withdrawals reduce water volumes in the environment and can decrease the capacity of the environment to both sustain plants and animals in the ecosystem and to meet human needs, including drinking water, hygiene, recreation, and transportation. Reductions in water flows or the resulting changes in the ecosystem may also affect the soil structure, the local climate, and even water quality by increasing the relative concentration of pollutants, among many other potential impacts.

Science-based targets for water quantity are calculated so that environmental flows are maintained in each basin; these are the minimum water flows required to sustain ecological processes and safeguard habitat and other requirements for the survival of species. Thresholds for groundwater can safeguard freshwater connectivity by averting groundwater depletion.

Other pressures on water quantity, such as the use of rainwater, disruptions in water systems from infrastructure (including dams), and the diversion of water volumes between basins are not covered by the current version of the methods.

In terms of water quality, nutrient pollution is the focus of the current version of Step 3 methods, specifically the loading of nitrogen and phosphorus.

Nitrogen and phosphorus, found naturally in water and soil, are essential for the growth of all living organisms, including aquatic life. However, in large concentrations, these nutrients result in fast and excessive growth of organisms such as algae and cyanobacteria. As these organisms eventually die, the decomposition of their biomass depletes the oxygen dissolved in water systems, leading to the asphyxiation of other aquatic life. This process, called eutrophication, may also release toxins into the environment (if produced by algae and cyanobacteria) and block the sunlight from other aquatic plants. Eutrophication may extend beyond freshwater systems to coastal areas as oxygen-depleted water flows down rivers and into the ocean.

Science-based targets for water quality are calculated so that nutrient concentrations in water systems remain below the threshold that leads to excessive growth of algae and cyanobacteria, avoiding the effects of eutrophication.

Other elements and activities that affect water quality are out of scope of the current methodology, including the loading of other pollutants (beyond nutrients) as well as activities that affect turbidity (e.g., sediment release) or change the water temperature (e.g., release of cooling water).