In addition to identifying targets and goals, factors that are likely to affect the conservation and management of these targets are also identified.

Threats and human use factors steer site selection to areas where the biological and physical targets are likely to be in better condition, where there are fewer human use conflicts, and where the overall suitability of conservation and management is higher (i.e. more financially feasible). For instance, an area that has been extensively developed or contains numerous pollution sources might be less suitable for biodiversity in general than an area that has been less developed. It may be more costly to achieve conservation in such areas as well. Examples of these factors include degraded water quality, shoreline hardening (seawalls, jetties), indicators of high use areas (docks, moorings, marinas), shipping lanes and oil rigs.

It is important to transparently illustrate how each threat or human use affects the targets of concern. For example, seagrass beds are directly affected by coastal development and in particular the establishment of shoreline hardening. Managers and practitioners can decision support information to identify the relative distributions of both the target and the impact to that target.

These individual factors are then compiled and weighted into a suitability index. It is often helpful during the Site Selection process to run separate scenarios with and without the inclusion of this index so that users can examine how this changes the results.