Secondary vs Tertiary Treatment Under the EU Directive

Introduction

The terms secondary treatment and tertiary treatment are often used together, but they serve different purposes in an urban wastewater treatment plant. Under the recast Urban Wastewater Treatment Directive (Directive (EU) 2024/3019), secondary treatment addresses biodegradable organic matter, while tertiary treatment adds nutrient removal where the Directive requires it.

For operators, municipalities and design engineers, the distinction matters because it drives process selection, footprint, operating strategy and upgrade sequencing. It also affects how a plant is assessed against the EU-wide framework and how future compliance risk is managed. For an overview of the legislative context, see /eu-directive.

What the Directive means by secondary treatment

The recast Directive defines secondary treatment as treatment that generally involves biological treatment with a secondary settlement stage, or another process that removes biodegradable organic matter.

In practical terms, this includes the mainstream biological processes used to reduce the organic load in municipal wastewater, such as:

• activated sludge systems
• sequencing batch reactors
• biofilm-based biological processes where they achieve biodegradable organic matter removal
• integrated biological processes with clarification or equivalent separation

The Directive does not restrict secondary treatment to one process type. The key requirement is performance: the treatment must remove biodegradable organic matter to the required standard.

Secondary treatment standards in Annex I

The Directive’s Annex I sets the secondary-treatment effluent standards as follows:

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

These values are the regulatory reference points for secondary treatment performance under the EU framework. In design and operation, they are typically checked together rather than in isolation, because solids capture, biomass settling and process stability all affect the final effluent.

Where secondary treatment applies

Secondary (biological) treatment is mandatory for agglomerations of 2,000 p.e. and above. The obligation is extended to agglomerations of 1,000 p.e. and above by 31 December 2035, with transitional and exemption arrangements, including for certain coastal areas and for Bulgaria, Croatia and Romania.

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

This definition matters because the Directive uses p.e. thresholds to determine the scope of treatment obligations. In plant planning, p.e. should be treated as a regulatory sizing basis, not as a substitute for hydraulic capacity or actual mass loading in design.

What tertiary treatment adds

Tertiary treatment is an additional treatment stage beyond secondary treatment. Under the recast Directive, it is associated with the removal of nitrogen and phosphorus, rather than simply biodegradable organics.

This is the point at which the process objective shifts from carbon removal to nutrient control. That change typically affects aeration strategy, recycle flows, chemical dosing, sludge production and process control requirements.

When tertiary treatment is required

The Directive sets two main obligations for nutrient removal:

• plants of 150,000 p.e. and above: tertiary treatment required by 2039
• plants of 10,000 p.e. and above in areas at risk of eutrophication: tertiary treatment required by 2045

These are Directive-level obligations. The way they are translated into permits, catchment plans and project programmes will depend on national transposition and local implementation.

Why tertiary treatment is different from secondary treatment

Secondary treatment is primarily about reducing organic pollution and suspended solids. Tertiary treatment is about polishing the effluent for specific nutrient objectives.

In engineering terms, that difference usually means:

• longer and more controlled biological reaction times, or additional treatment zones
• tighter dissolved oxygen and recirculation control
• internal carbon balance considerations
• possible chemical phosphorus removal support
• greater sensitivity to seasonal temperature and influent variability

Secondary treatment can often be judged against a relatively direct compliance target. Tertiary treatment tends to be more process-dependent, because nutrient removal performance is affected by site-specific influent characteristics, available footprint and operating regime.

Secondary versus tertiary: the practical distinction

The simplest way to separate the two is by their treatment objective.

Secondary treatment

Secondary treatment is the core biological treatment stage. Its purpose is to remove biodegradable organic matter and, together with clarification or equivalent separation, produce effluent meeting the Annex I secondary standards.

Typical operational focus:

• stable biomass concentration
• sludge settleability
• adequate oxygen transfer
• control of hydraulic and organic shock loads
• consistent secondary clarification performance

Tertiary treatment

Tertiary treatment is an added stage for nutrient removal. Its purpose is to reduce nitrogen and phosphorus where the Directive requires it.

Typical operational focus:

• nitrification and denitrification control
• phosphorus removal strategy, biological and/or chemical as appropriate to the site
• recycle management
• process monitoring for nutrient compliance
• managing the interaction between nutrient removal and sludge handling

The two stages are therefore sequential and complementary, not interchangeable. A plant may meet secondary standards without having nutrient removal capability. A plant with tertiary treatment must still achieve reliable secondary performance upstream.

Engineering implications for WWTP upgrades

For existing works, the main question is usually not whether secondary treatment exists, but whether it is sufficient for the future regulatory scope and the current load profile.

Key assessment points include:

• current agglomeration size in p.e. and projected growth
• whether the plant already meets Annex I secondary standards consistently
• available footprint for biological expansion or reconfiguration
• process type and whether it can be adapted for nutrient removal
• influent industrial contribution and variability
• secondary clarifier capacity and solids separation performance
• sludge age, aeration capacity and internal recycle capability

Where a plant is already close to the secondary limits, upgrading for tertiary treatment may require careful sequencing. For example, changes intended to improve nitrogen removal can affect sludge production, oxygen demand and clarifier loading. The process should therefore be assessed as a whole rather than by adding a single treatment step in isolation.

Indicative design considerations

Design values for biological treatment are site-specific, but common practice is to evaluate:

• dissolved oxygen setpoints as a process-control range rather than a fixed universal value
• sludge age and MLSS as operating variables linked to temperature, loading and treatment objective
• F/M ratio as an indicator of process intensity
• detention time, recycle ratio and reactor zoning for nutrient removal suitability

These are indicative engineering considerations, not universal compliance numbers. Actual design and control targets should be set from the influent characterisation, required effluent quality, climate and available treatment train.

Compliance strategy under the recast Directive

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

For plant owners and designers, this means the regulatory direction is already clear, even though national implementation details will still vary. The main compliance question is how a site will move from its current treatment level to the required one within the applicable timetable.

A pragmatic strategy is to separate the work into stages:

• confirm current treatment level and performance record
• identify the applicable p.e. threshold and receiving-water context
• check whether the site is already within the scope of tertiary obligations, or will enter it later
• assess whether secondary capacity, clarification and sludge handling are robust enough for future upgrades
• develop an upgrade pathway that protects compliance during construction and transition

For many plants, the most efficient first step is a structured process review. If you need a site-specific starting point, you can Start the Engineering Assessment.

How this applies to your plant

If your plant only provides secondary treatment, the first question is whether it reliably meets the Annex I secondary standards and whether it falls within the current or future p.e. thresholds in the Directive.

If your plant already has nutrient removal, the key issue is whether the biological process is robust enough to sustain tertiary performance under variable loads and seasonal conditions.

In either case, the right approach is to evaluate the plant against:

• current effluent performance
• process configuration and spare capacity
• future regulatory scope under the recast Directive
• likely upgrade complexity for nutrient removal
• operational risks during transition

Secondary and tertiary treatment are not just legal labels. They define different engineering objectives. A plant that understands that distinction can plan upgrades more effectively, reduce compliance risk and choose the least disruptive route to future performance.