EU Wastewater Directive 2039: Secondary Treatment Requirements

EU Wastewater Directive 2039: what the 2039 framework means for secondary treatment

The recast Urban Wastewater Treatment Directive, Directive (EU) 2024/3019, changes the planning horizon for wastewater utilities and consulting engineers across the European Union. For secondary treatment, the key message is straightforward: biological treatment remains the core compliance step for municipal wastewater, and the obligation is widening from larger agglomerations to smaller ones over time.

This article focuses on the secondary-treatment requirements relevant to the 2039 planning horizon, with the practical implications for existing plants, expansion projects and treatment upgrades. For the broader legal context, see the EU directive overview.

1) The regulatory timeline that matters

Several dates shape how plants should plan.

• The recast directive entered into force on 1 January 2025.
• It repeals Directive 91/271/EEC with effect from 1 August 2027.
• Member States must transpose the recast directive into national law by 31 July 2027.

For operators, this means the legal framework is already in place, but national implementation details may still evolve during transposition. Engineering teams should therefore plan against the EU framework while tracking national rules as they are adopted.

2) What counts as secondary treatment?

Under the recast directive, secondary treatment is defined as treatment that generally involves biological treatment with a secondary settlement stage, or another process that removes biodegradable organic matter.

In practical plant terms, this covers the familiar biological routes used in municipal wastewater treatment, including:

• activated sludge systems;
• oxidation ditches;
• sequencing batch reactors;
• biological filtration or attached-growth processes where they are used to remove biodegradable organics;
• other equivalent biological processes that achieve the same function.

The directive definition is functional rather than prescriptive. It does not lock plants into one process configuration, but it does require that the selected process reliably removes biodegradable organic matter and meets the applicable effluent standards.

3) Which agglomerations must provide secondary treatment?

The obligation is based on population equivalent, or p.e. A p.e. is the organic biodegradable load having a five-day biochemical oxygen demand (BOD5) of 60 g of oxygen per day.

The current and future scope is as follows:

• Secondary biological treatment is mandatory for agglomerations of 2,000 p.e. and above.
• That obligation is extended to agglomerations of 1,000 p.e. and above by 31 December 2035.
• Transitional and exemption arrangements apply in certain cases, including for some coastal areas and for Bulgaria, Croatia and Romania.

For design and planning teams, this is important because small and medium agglomerations that have historically relied on simpler treatment or limited treatment may need to progress towards full biological secondary treatment before the end of 2035.

The practical implication is not just construction of new tanks or package plants. It also affects:

• collection system and hydraulic balance;
• stormwater and infiltration management;
• sludge handling capacity;
• process stability during wet-weather peaks;
• operator competence and monitoring systems.

4) The Annex I effluent standards for secondary treatment

Annex I sets the secondary-treatment effluent standards used for compliance assessment.

The standards are:

• BOD5: 25 mg/L, or 70-90% reduction;
• COD: 125 mg/L, or 75% reduction;
• TSS: 35 mg/L.

These values matter because they define the performance envelope for the biological stage and its downstream clarification or solids separation. In practice, the secondary settlement stage is often the limiting factor when plants struggle with solids carryover, filamentous bulking, hydraulic overload or peak wet-weather flows.

From an engineering perspective, compliance with these standards depends on more than the biological reactor itself. The following elements are commonly critical:

• influent equalisation and flow management;
• oxygen transfer and aeration control;
• sludge age and biomass retention;
• secondary clarifier sizing and loading;
• return activated sludge and waste sludge control;
• process instrumentation and online monitoring;
• robustness under low-temperature and shock-load conditions.

Because the directive sets outcome-based standards, plants should review the whole treatment train rather than treat aeration or reactor volume in isolation.

5) What 2039 means in the broader compliance pathway

The 2039 horizon is important because it sits between secondary-treatment compliance and the later nutrient and micropollutant requirements.

Under the recast directive:

• tertiary treatment for nitrogen and phosphorus removal is required for plants of 150,000 p.e. and above by 2039;
• that nutrient-removal obligation also applies to plants of 10,000 p.e. and above in areas at risk of eutrophication by 2045;
• quaternary treatment for micropollutant removal is required for plants of 150,000 p.e. and above by 2045, with interim milestones in 2033 and 2039;
• energy neutrality for the urban wastewater treatment sector is to be achieved by 2045.

For many utilities, this means the secondary-treatment upgrade strategy cannot be planned independently from the next layers of treatment. Site layouts, spare land, hydraulic profile, pumping capacity and sludge line upgrades should be considered together, because future tertiary or quaternary additions may be constrained by the same footprint and hydraulic limits.

However, this article keeps the focus on secondary treatment. The key point is that a plant that only barely meets present-day biological performance may find it difficult to serve as a stable platform for future nutrient or micropollutant upgrades.

6) Design and operational implications for existing plants

The directive does not prescribe a single process design, but it does create a clear performance obligation. For operators and consulting engineers, the main question is whether the existing plant can reliably meet the Annex I standards across normal and adverse conditions.

Typical engineering review items include:

Biological reactor capacity

• Is the present process volume adequate for current and projected loads?
• Is the biomass age window appropriate for stable carbon removal?
• Are there seasonal temperature effects that reduce treatment margin?

Secondary clarification and solids separation

• Is clarifier capacity adequate for peak wet-weather flow?
• Is sludge settling behaviour stable?
• Are solids washout events causing exceedances of TSS or BOD5?

Aeration and oxygen transfer

• Does aeration capacity match organic loading and diurnal variation?
• Is control based on dissolved oxygen, ammonia, or a combination where relevant?
• Are blowers and diffusers maintaining performance over time?

Hydraulic resilience

• Does the plant retain compliance during storm flow or infiltration episodes?
• Are bypasses, equalisation or flow-splitting arrangements sufficient?
• Can critical units be taken out of service without compromising compliance?

Monitoring and control

• Are sampling points representative?
• Is the monitoring regime adequate to demonstrate compliance with Annex I?
• Does the plant have enough process data to support optimisation and investment decisions?

Indicative design values such as dissolved oxygen, sludge age, mixed liquor suspended solids, or food-to-microorganism ratio are site-specific. They can be useful for diagnosis and optimisation, but they should be treated as plant-specific operating targets rather than universal compliance numbers.

7) How operators should prepare now

The most effective preparation is a structured gap assessment against the directive, combined with a process audit of the current plant.

A practical review should cover:

• current p.e. served and projected growth;
• whether the agglomeration already falls within the 2,000 p.e. threshold;
• whether the site will come within the 1,000 p.e. threshold by 2035;
• current effluent performance against BOD5, COD and TSS;
• wet-weather performance and solids carryover risk;
• available space for future tertiary or quaternary stages;
• sludge line capacity and disposal route resilience;
• energy use and opportunities for process efficiency.

This is also the right point to confirm the national implementation position, because member states will transpose the directive into their own legal frameworks by 31 July 2027. The EU requirements set the direction, but permitting, compliance assessment and local programme delivery will depend on national law and competent authority practice.

If you need a structured first pass, Start the Engineering Assessment to review plant size, treatment performance and upgrade implications.

How this applies to your plant

If your plant serves an agglomeration near or above 2,000 p.e., secondary treatment is already part of the compliance baseline. If your catchment is smaller today but could exceed 1,000 p.e. by 2035, the planning question is no longer whether biological treatment will be needed, but how and when it should be implemented.

For existing plants, the immediate task is to verify whether the biological stage and secondary settlement can reliably meet Annex I standards under realistic operating conditions. For municipalities and consultants, the longer-term task is to ensure that any investment made now will remain compatible with the 2039 and 2045 pathway.

A focused engineering review should therefore look at:

• compliance margin at present loads;
• hydraulic robustness in wet weather;
• solids separation performance;
• footprint for future upgrades;
• integration with sludge and energy systems.

For a structured next step, Start the Engineering Assessment and benchmark your plant against the current secondary-treatment requirements and the likely upgrade pathway ahead.