Understanding Scotland’s Protected Species Licensing Framework

Scotland’s protected species licensing framework underpins ecological decision-making across development planning, construction, land management, and infrastructure delivery. Understanding how licensing works, when it is required, and how evidence is assessed is essential for project managers, planners, architects, and contractors. Incorrect assumptions about licensing are a common cause of avoidable delay; by contrast, well-timed engagement with ecologists and regulators enables proportionate, legally compliant outcomes.

This article outlines the purpose, structure, and application of protected species licensing in Scotland, focusing on key species groups relevant to development projects and the evidential thresholds that influence regulatory decisions.

1. Legislative foundation

The core legislation governing protected species in Scotland is the Conservation of Habitats and Species Regulations 2017 (as amended in Scotland) and the Wildlife and Countryside Act 1981. These establish offences relating to killing, injuring, or disturbing certain species, and damaging or destroying their breeding sites and resting places (Scottish Government 2019; NatureScot 2020). The Regulations implement Scotland’s obligations under the Habitats Directive and apply to European Protected Species (EPS), including bats, otter, pine marten (in certain contexts), and great crested newt.

Licensing functions sit with NatureScot, which determines whether derogation from normal legal protection is allowable. Licensing does not remove the protection afforded to species; it provides a controlled legal route for activities that would otherwise constitute an offence.

2. When a licence is required

A licence is required when an activity is likely to deliberately or unintentionally:

• disturb EPS,

• risk injury or mortality, or

• damage or destroy a breeding site or resting place.

For bats, this includes works affecting roost structures or access points, regardless of season. For otter, it may include culvert works, bank stabilisation, or activities affecting holts or couches. For great crested newts (where present in Scotland), it may involve pond removal or terrestrial habitat loss.

A common misconception is that the absence of visible animals means that licensing is unnecessary. In practice, roosts, holts, and other resting places remain protected even when unoccupied (NatureScot 2020). This principle is central to risk management during pre-construction planning.

3. The three licensing tests

For European Protected Species, NatureScot applies three statutory tests:

Test 1: Purpose

The activity must serve a purpose specified in legislation, most commonly “imperative reasons of overriding public interest” or “preserving public health or safety”. Development projects with planning permission can meet this test, though it is not automatic.

Test 2: No satisfactory alternative

The applicant must demonstrate that alternative designs, methods, or timings have been considered and discounted on clear grounds. Evidence of iterative design is essential.

Test 3: Favourable conservation status (FCS)

The proposed activity must not negatively affect the conservation status of the species at local or wider scales. This is where ecological evidence, survey data, and mitigation design become critical. Projects that cannot demonstrate maintenance of FCS may be refused a licence.

4. Evidential requirements and survey robustness

NatureScot licensing decisions depend on robust ecological evidence demonstrating:

• species presence or likely absence;

• level of risk posed by the works;

• scale and functional importance of resting places or territories;

• ecological reasoning supporting mitigation and compensation.

Survey limitations must be explicitly acknowledged. For example, partial access to roof voids, weather disruptions in bat surveys, or seasonal constraints affecting otter holt activity should be documented transparently. Regulators expect evidence-based interpretation, not definitive assertions where evidence is incomplete.

Projects commonly encounter delay when survey effort is insufficient or when species presence is identified too late in the design or tendering process.

5. Mitigation, compensation, and licensing conditions

Licences require a clear and deliverable mitigation plan. For EPS, this may include maintaining roost functionality, providing alternative resting sites, controlling lighting impacts, or phasing works to avoid sensitive periods. Compensation is considered where functionality cannot be fully retained.

Licences often contain post-construction monitoring requirements, reflecting NatureScot’s emphasis on ensuring outcomes align with predicted impacts (NatureScot 2020).

6. Early engagement reduces risk

Early ecological assessment significantly increases the likelihood of a licence being granted where one is required. Identifying constraints at feasibility or concept design stage enables:

• proportionate survey planning,

• avoidance of high-risk design features,

• realistic programme sequencing, and

• early dialogue with regulators where needed.

Late discovery of EPS constraints often necessitates rapid survey mobilisation, redesign, or seasonal delay. Understanding licensing principles early in a project’s lifecycle prevents these issues and supports legal compliance.

Conclusion

Protected species licensing in Scotland provides a structured, evidence-based mechanism for enabling necessary development while safeguarding vulnerable species. Projects that recognise licensing requirements early, invest in sound ecological evidence, and design with protected species in mind encounter fewer constraints and deliver more predictable outcomes. Licensing is not a barrier to development; it is a framework for responsible and legally compliant project delivery.

References

NatureScot 2020. Species Licensing: Guidance Notes for Protected Species. NatureScot, Inverness.
Scottish Government 2019. Wildlife Crime and Protected Species. Scottish Government, Edinburgh.
JNCC 2019. Protected Species and Licensing in the UK: Legislative Overview. Joint Nature Conservation Committee, Peterborough.