AquaPri (2023): Conservation of natural habitats and of wild fauna and flora (Natura 2000) and activity of fish farming

  • Leonor Neves


The CJEU has a consistent engagement with Article 6 of the Council Directive 93/43/EEC of 21 May 1992 on the conservation of natural habitats and of wild fauna and flora[1] (the Habitats Directive), as amended, highlighting its enduring importance in preserving Europe’s biodiversity. There are challenges faced by national authorities in enforcing the directive, leading to occurrences where projects are authorized with breaches of its provisions, notably Article 6(3).

This analysis centers around the CJEU’s recent AquaPri judgment, addressing the consequences of breaches under Article 6(3). While the full implications are yet to be determined, it’s important to clarify that the judgment does not mandate extensive assessments for all previously authorized projects. Instead, it provides valuable insights into existing case law on Article 6 of the mentioned directive, focusing on key issues like the definition of ‘project’ and the responsibilities of Member States in remedying assessment failures. 

Throughout this essay, we’ll discuss several important questions raised by the CJEU during this case, namely: the scope of the concept of ‘project’ determined in the mentioned provision; the consequences that may fall upon a member state in case of a breach; and the relevance of an environmental assessment carried out by another entity.

Legal background

The CJEU identifies the relevant legal background in the analyzed case note.  European Union Law

  • The tenth recital in the preamble to Directive 92/43/EEC
  • Article 6(1) to (3) of Directive 92/4/ECC Danish Law 
  • Law on environmental protection: paragraph 33(1) and paragraph 35
  • The habitats decree: paragraph 6(1) and (2), which transposed into Danish law Article 6(3) of Directive 92/43/EEC, and paragraph 7(7)
  • The authorization decree: paragraph 70(2) and annex 2

Relevant Facts and Summary of the Case

In 2006 AquaPri, the owner of a fish farm situated in Småland’s bay near to a Natura 2000 site, seeks permission to increase its nitrogen emissions. The permission was granted, by a decision which was adopted on 27 October 2006.  

This decision was challenged before the relevant review body, which found that it was vitiated in its assessment. The problem was that the competent authority, during the required assessment, analyzed the impact of the nitrogen emissions in the Natura 2000 site individually, when it should also have taken into account three close by projects (also fish farms), and the impact that they cumulatively would have in the mentioned bay. The Court decided that the fact did not justify annulment of the decision. 

The same decision also required AquaPri to submit, by 15 March 2014 at the latest, an application for authorization under Paragraphs 33 and 35 of the Law on environmental protection, as provided for in Paragraph 70(2) of the Authorization Decree, the company made an application to that effect.

By decision of 16 December 2014, the competent authority granted the authorization requested by AquaPri after noting that the amount of nitrogen emitted by the operation belonging to it remained unchanged and that it was apparent from an assessment carried out after the adoption of that decision (by National River Basin Management Plan) that that operation and the three neighboring projects, considered in combination, were not likely to have a significant effect on the Natura 2000 site from which they are located.

The decision was contested. The Board of Appeal annulled it in 2018, stating that it lacked proper assessment, according to article 6(3) of Directive 92/43/EEC, which could result in possible harm to the mentioned bay. The Board of Appeal also found that an assessment carried out later by another entity does not affect the obligation of the competent authority to carry out a proper assessment, pursuant to Article 6(3) of Directive 92/43/EEC.

AquaPri contested the decision before the competent court, which itself forwarded the case to the referring court (High Court of Eastern Denmark). The referring court raises the problem around the definition of the term ‘project’ in article 6 of Directive 92/43/EEC. Considering these circumstances, the Østre Landsret (High Court of Eastern Denmark) decided to stay the proceedings and to refer the following questions to the Court of Justice of the European Union for a preliminary ruling: 

1.     Is [the first sentence of] Article 6(3) of Council Directive [92/43] to be interpreted as being applicable to a situation, such as that in the present case in which an authorization is sought to continue operation of an existing fish farm, where the activity of the fish farm and the discharge of nitrogen and other nutrients remains unchanged in relation to the activity and discharge authorized in 2006, but where no assessment was made of the overall activity and the cumulative effects of all the fish farms in the area, the competent authorities having merely assessed the increase in the discharge of nitrogen and other substances from the fish farm concerned? 

2.     Is the fact that the National River Basin Management Plan 2015-2021 takes account of the presence of the fish farms in the area, in so far as it sets aside a specific amount of nitrogen to ensure that the existing fish farms in the area can make use of their present discharge authorizations and that the actual discharge from the fish farms remains within the set limits, relevant, for the purposes of answering the first question? 

3.     If, in a situation such as that in the present case, an assessment must be carried out pursuant to [the first sentence of] Article 6(3) of Directive [92/43], is the relevant authority required to take into account in such an assessment the limits

on the discharge of nitrogen set aside in the River Basin Management Plan 20152021 and any other relevant information and assessments which might arise from the River Basin Management Plan or the Natura 2000 plan for the area?’

For the first question, the court considered that, under normal circumstances, an authorization for continuation like the one granted to AquaPri in 2014, would not be subject to a new proper assessment pursuant Article 6(3) of Directive 92/43/EEC. Considering that the original assessment, carried out in 2006, was not properly done, since it did not consider the nearby projects and all its effects cumulatively, there should have been a new assessment with the requirements of that provision (Article 6(3)). 

For the second and third questions, the court concludes that the assessment must be taken into consideration if it satisfies some specific criteria, meaning that it must be complete, accurate and definitive. It also states that it is for the referring court to analyze if such criteria are fulfilled.  

Critical analysis 

The concept of project under article 6(3) of the Habitats Directive 

In the present case, the referring court is uncertain whether the authorization granted to AquaPri is to be included in the concept of ‘project’ within the meaning of Article 6(3) of the Habitats Directive. 

In a previous case law[2], the court has stated that the renewal of an existing permit cannot, in the absence of any works or interventions involving alterations to the physical aspect of the site, be classified as a ‘project’ within the meaning of the provisions preceding Article 1(2)(a) of the Directive 2011/92/EU of the European Parliament and of the Council of 13 December 2011 on the assessment of the effects of certain public and private projects on the environment (the EIA Directive). It is important to note that, in that same judgment, the Court clarified the definition of the concept of ‘project’ within the meaning of Article 1(2) of Directive 85/337/EEC3 and, in particular, the requirement for an ‘intervention in the natural surroundings’ contained therein. Although, the mentioned requirements are not found in Article 6(3) of the Habitats Directive. Thus, Article 1(2)(a) of the EIA Directive defines the concept of ‘project’ for the proposes of that provision, attaching to it conditions that are not specified in the equivalent provision of the Habitats Directive.

In this same judgment, it is concluded that if the definition of ‘project’ according to Directive 85/337/EEC is more restrictive than the definition of ‘project’ according to the Habitats Directive, it would imply that an activity considered a ‘project’ by Directive 85/337/EEC, will, a fortiori, be considered a ‘project’ the Habitats Directive. However, this does not mean that if an activity is not considered a project under the EIA Directive, it will not be considered a project under the Habitats Directive, since the second one has a broader scope.

We can thus conclude that, in order to determine whether an authorization such as the one granted to AquaPri may be classified as a ‘project’ within the meaning of Article 6(3) of the Habitats Directive, it is important to examine whether such activities are likely to have a significant effect on a protected site.

The 10th recital of the Habitats Directive states that an appropriate assessment must be made of any plan or program likely to have a significant effect on the conservation objectives of a site which has been designated or is designated in future. That recital finds expression in Article 6(3) of the directive, which provides, inter alia, that a plan or project likely to have a significant effect on the site concerned cannot be authorized without a prior assessment of its implications for that site[3].

The court determined that the authorization granted to AquaPri in 2014 did not fall within the scope of the concept of ‘project’ established in the Habitats Directive, and, therefore, was not, a priori, subject to a new assessment under the conditions of Article 6(3). 

In my view, the Court appears to diminish the practical content of the obligation to renew the authorization granted to AquaPri in 2006 by the competent authority. This obligation suggests a need to reassess the project, possibly because the respective environmental impacts must be reevaluated. There is a rationale behind this obligation, that the Court seems to have overlooked, which is to ensure that the project remains sustainable and does not have harmful effects on the nearby Natura 2000 site. There would be no practical purpose in renewing an authorization if it was not anticipated that the effects of the respective activity may have changed, or that it is possible to reduce its negative impacts.

It is essential to note that, in determining the broadness of the concept of project, the court references another case law that raised concerns about the scope of this concept[4]. I must point out that, after a thorough analysis, the comparison between the two situations seems somewhat strained. While both cases concern the scope of application of the term ‘project’ under Article 6(3) of the Habitats Directive, they start from very different circumstances. In the cited case, we are discussing organic fertilizers and other elements that can potentially be controlled by people. This means that the amount of fertilizer reaching the fields and its respective environmental impact are entirely predictable. However, when discussing nitrogen release dependent on a species development, which can be easily influenced by poorly planned breeding seasons or specimen growth, there is some instability involved. In the AquaPri case, we are dealing with living organisms, their development, and reproduction, as sources of pollutant emissions. There will always be an element of unpredictability associated, which should not be overlooked. Depending on the human being is completely different than depending on nature, this why it is concluded that in the case of AquaPri, the need for a new assessment under Article 6(3) is much more evident when compared to the mentioned case.

In conclusion, I posit that, in order not to disregard the actions of the competent authority, the Court should have considered the authorization granted to AquaPri as a project in accordance with the definition provided in the already mentioned provisions. It cannot be definitively concluded that the activity at hand remains harmless to the Natura 2000 network site in question. Nevertheless, the Court concludes that the original authorization was unlawful, as a proper assessment was not conducted. The court ultimately concludes that the 2016 authorization subsequent to the EIA should have been preceded by an assessment in accordance with the requirements of Article 6(3).

The consequences that may fall upon a member state in case of a breach 

Despite our position, the court deemed that the authorization granted to AquaPri in 2014 did not encompass the concept of a project as outlined in Article 6(3) of the Habitats Directive. Therefore, it would not, a priori, be subject to a new assessment under Article 6(3). However, the court determined and concluded that the assessment conducted during the project approval did not meet the legal requirements. Additionally, the court also considered that, in the type of authorization in question, the exclusion of the need for a new assessment is contingent upon the proper execution of the initial assessment, which did not occur. Considering this, we cannot, by any means, dismiss the necessity of a new assessment.  

Additionally, the occurrence of a breach of the already mentioned provision cannot proceed without any legal consequences. Article 4(3) of the Treaty on European Union (TEU) becomes relevant in this context, stipulating, through the principle of cooperation, that states must take all necessary measures to ensure compliance with the execution of obligations arising from the EU law.

So, it is safe to say that there was a violation committed by the competent Danish authority, raising an issue of liability, as this failure may have resulted in environmental consequences and generated unfair positions, particularly in the economic sector.

Once again referring to a previous case law[5], the court states that in cases where a project has been authorized without complying with the environmental assessment requirements of Directive 92/43/EEC, the competent national authority must conduct a subsequent review based on Article 6(2) of that directive. This review aims to prevent any deterioration or disturbance that could significantly affect the relevant site. However, such a review is not the sole measure the authority may take. EU law allows the authority to revoke or suspend the granted authorization for a new assessment, provided it occurs within a reasonable timeframe, considering the reliance of the concerned party on the initial authorization’s lawfulness. 

In specific cases under national law[6], the authority may also regularize the situation. When a Member State mandates a new authorization for the continuation of an already approved activity, the competent national authority must subject it to a new assessment if the previous one was non-compliant. In the present case, the authorization issued in 2006 required a new application for authorization by 15March 2014, under the Danish Law on

Environmental protection[7], indicating an awareness of the need for reevaluation. The 2006 assessment failed to meet the requirements of Article 6(3) of Directive 92/43/EEC, focusing only on the individual impact and not considering the project’s combined effects. Regardless of the measure used to remedy the breach, the Member State responsible may be held liable for damages if the authorization is revoked or amended, as in the AquaPri case, and it is for the competent national court to verify this liability.

The court’s ruling appears nothing short of reasonable, as the breach stems from a national authority subject to the jurisdiction of national courts. Regardless of national legislation, the Member State must be held liable for the mistake to comply with the provisions of Article 4(3) of the Treaty on European Union (TEU), that establishes the principle of cooperation, mandating that Member States take all necessary general or specific measures to ensure the compliance with obligations arising from the European Union law.

The relevance of an assessment carried out by another entity

The third issue arises with the existence of a program-based impact assessment conducted retroactively. In this regard, the court addresses two questions: the requirement for this assessment to be taken into account to determine the need for a new assessment and the necessity for this assessment to be considered in the event of conducting a new assessment. 

In this regard, the court states that when deciding whether a plan or project needs an assessment according to Article 6(3) of Directive 92/43/EEC, previous assessments can be considered if they are relevant, complete, accurate, and definitive. However, relying on previous assessments alone cannot rule out the possibility of significant adverse effects if scientific and environmental data haven’t changed and if there are other plans or projects not considered correctly[8]. 

The court emphasizes that, at the time of making a decision on plan authorization, there should be no reasonable scientific doubt regarding the absence of adverse effects on the site[9]. These principles apply even when a Member State requires a new authorization for a previously authorized activity, and the competent national authority should consider relevant previous assessments. The authority must also consider all factors and implications since the initial authorization, similar to an ex post facto examination[10]. The court concludes that it’s up to the referring court to determine if previous assessments meet the requirements and what conclusions should be drawn for authorizing the continuation of the activity.

Consequently, the Court states that a new assessment will not be necessary if previous assessments meet the requirements of the Habitats Directive. This decision makes perfect sense from a procedural economy standpoint. A new environmental assessment could become a significant expenditure of time and resources. However, as concluded by the court, in the case of AquaPri, it makes perfect sense for it to occur.


This essay allowed me to analyze and consider highly relevant issues. The authorization of unlawfully projects in light of European Union law is a constant reality, as it is challenging to reconcile all national law with European Union law. More than an issue of reconciling national and European law, this case hinges on the misapplication of the law, in this case, the lack of appropriate assessment following the requirements of article 6(3) of the Habitats Directive. It is considered that the CJEU has done an excellent job of weighing and relating to different cases previously analyzed. Despite very minor divergences, there is no disagreement with what has been decided.

Peer-Reviewed by:

[1] Directive – 92/43 – EN – Habitats Directive – EUR-Lex (  

[2] judgment of 17 March 2011, Brussels Hoofdstedelijk Gewest and Others (C-275/09, EU:C:2011:154) 3 EUR-Lex – 31985L0337 – EN – EUR-Lex (

[3] judgment of 12 April 2018, People Over Wind and Sweetman, C-323/17, EU:C:2018:244, paragraph 28.

[4] Judgment of 7 November 2018, Coöperatie Mobilisation for the Environment and Others (C-293/17 and C-294/17, EU:C:2018:882

[5] judgment of 14 January 2016, Grüne Liga Sachsen and Others, C-399/14, EU:C:2016:10, paragraphs 61 and 62.

[6] CURIA – Documents (

[7] Paragraph 70(2) of the Godkendelsesbekendtgørelsen (Bekendtgørelse nr. 1458 om godkendelse af listevirksomhed) (Decree No 1458 on the approval of activities subject to authorisation) of 12 December 2017 (‘the Authorisation Decree’) states: ‘Existing establishments covered by points I 203, I 205 … of Annex 2 which are not approved under Paragraph 33 of the Law on environmental protection shall submit applications for authorisation in accordance with the rules laid down in the present Decree by 15 March 2014 at the latest.’

[8] judgment of 9 September 2020, Friends of the Irish Environment, C-254/19, EU:C:2020:680,

[9] judgment of 17 April 2018, Commission v Poland (Białowieża Forest), C-441/17, EU:C:2018:255

[10] judgment of 14 January 2016, Grüne Liga Sachsen and Others, C-399/14, EU:C:2016:10

  • Leonor Neves