Primary vs Secondary vs Tertiary Treatment in the EU Directive

Introduction

Wastewater treatment is usually described in stages: primary, secondary and tertiary. For operators and engineers, those labels are useful, but they can also be misleading if they are treated as interchangeable. Each stage serves a different purpose, removes different pollutants and has a different role in meeting the EU Urban Wastewater Treatment Directive.

Under Directive (EU) 2024/3019, secondary treatment is the key biological stage. It is the regulatory baseline for many agglomerations, and the requirements widen further over time. Primary treatment remains an important front-end step in some systems, while tertiary treatment is added where nutrient removal is required. Understanding the differences matters for compliance, process selection and upgrade planning.

For a broader view of the legal framework, see the EU Directive overview.

What primary treatment does

Primary treatment is a physical separation stage. Its purpose is to remove materials that can be settled or skimmed before biological treatment.

Typical functions of primary treatment

• Remove settleable solids by gravity settling
• Remove floatables, oils and grease by skimming
• Reduce the solids load to downstream processes
• Provide a more stable influent to biological treatment

In engineering terms, primary treatment is often associated with primary settlement tanks or primary clarifiers. In some treatment trains, primary treatment is limited or omitted, but where it exists it can reduce the burden on aeration and secondary clarification.

What primary treatment does not do

Primary treatment does not generally achieve the level of biodegradable organic removal expected from secondary treatment. It is not, by itself, the biological treatment stage envisaged by the directive definition of secondary treatment.

That distinction matters because 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 other words, the compliance focus is on the removal of biodegradable pollution, not only on sedimentation.

What secondary treatment does

Secondary treatment is the core biological stage in a municipal wastewater treatment plant. It is designed to remove biodegradable organic matter, usually through microbial processes.

Common biological treatment routes

• Conventional activated sludge
• Extended aeration systems
• Oxidation ditches
• Biofilm processes such as trickling filters or moving bed biofilm reactors
• Sequencing batch reactor arrangements

The specific process is less important than the outcome: the plant must provide effective biological oxidation or conversion of biodegradable organics, followed by separation of the biomass or another means of achieving the required effluent quality.

Regulatory role of secondary treatment

Under Directive (EU) 2024/3019, secondary biological treatment is mandatory for agglomerations of 2,000 p.e. and above. The obligation extends to agglomerations of 1,000 p.e. and above by 31 December 2035, subject to transitional and exemption arrangements, including for certain coastal areas and for Bulgaria, Croatia and Romania.

The directive also sets EU-wide secondary-treatment effluent standards in Annex I:

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

These are compliance values for the treatment stage, not design targets that can be applied blindly to every plant. Hydraulic pattern, influent strength, industrial contribution, stormwater ingress and seasonal loading all affect actual process behaviour.

Practical process implications

For an operator or designer, secondary treatment performance depends on:

• Adequate oxygen transfer and aeration control
• Sufficient biomass retention time
• Stable solids separation in the final clarifier or equivalent stage
• Control of filamentous growth and sludge settleability
• Effective handling of peak flow and peak load conditions

Indicative design and operating values such as dissolved oxygen, sludge age, MLSS and F/M ratio are site-specific and should be established from the selected process, loading profile and effluent objective. They should not be borrowed from another plant without verification.

What tertiary treatment adds

Tertiary treatment comes after secondary treatment and is generally added to remove pollutants that are not adequately controlled by the biological stage alone. In the EU directive context, the main focus is nutrient removal: nitrogen and phosphorus.

When tertiary treatment becomes relevant

The recast directive introduces specific nutrient-removal obligations:

• 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 requirements sit alongside the broader compliance framework and are separate from the secondary-treatment obligation. They reflect the need to protect receiving waters where nutrient enrichment is a concern.

Typical tertiary functions

• Nitrogen removal through nitrification and denitrification, or equivalent process arrangements
• Phosphorus removal through biological uptake, chemical precipitation, or a combination of both
• Polishing of suspended solids where needed to support downstream nutrient removal

For many plants, tertiary treatment is not a simple bolt-on unit. It may require changes to the upstream biological process, internal recycle flows, chemical dosing, sidestream handling or final clarification capacity.

Secondary versus tertiary in practice

Secondary treatment removes biodegradable organic matter. Tertiary treatment targets nutrients and, in some cases, further solids polishing. A plant may meet the secondary treatment requirement while still needing tertiary upgrades later.

That sequence is important for asset planning. A plant that is compliant today on carbon removal may still face future nutrient obligations depending on size and receiving-water sensitivity.

Primary, secondary and tertiary: the difference in one view

The three stages are best understood by the pollutant each one is meant to address.

Primary treatment

• Main role: physical removal
• Typical pollutants removed: settleable solids, floatables, oils and grease
• Regulatory purpose: front-end load reduction

Secondary treatment

• Main role: biological removal of biodegradable organic matter
• Typical pollutants removed: BOD and a significant proportion of COD and suspended solids
• Regulatory purpose: core compliance stage for many agglomerations

Tertiary treatment

• Main role: polishing and nutrient removal
• Typical pollutants removed: nitrogen, phosphorus and, in some cases, remaining solids
• Regulatory purpose: advanced protection of sensitive receiving waters

The practical sequence is often described as primary first, then secondary, then tertiary. But not every plant has all three stages. Some have primary and secondary only; others have an integrated biological process with limited primary settlement; and some smaller plants may use treatment trains that combine functions within one process line.

How the directive changes planning for treatment trains

The recast directive does not just set present-day rules; it also creates a pathway for future upgrades. That means the treatment-train question should be considered in stages.

Key planning points

• Verify the current population equivalent load and forecast growth
• Check whether the agglomeration falls within the 2,000 p.e. threshold now or the 1,000 p.e. threshold by 31 December 2035
• Review whether the receiving water or catchment is subject to eutrophication risk
• Assess whether current secondary treatment can be upgraded to meet future nutrient requirements
• Examine whether the existing primary settlement capacity supports a higher biological load

In many cases, the most economical option is not to add tertiary treatment immediately, but to ensure the secondary stage is robust enough to handle future loads and tighter effluent objectives.

Engineering assessment considerations

A structured review should cover:

• Influent characterisation, including biodegradable load and wet-weather variation
• Hydraulic capacity of primary and secondary units
• Biological process resilience under seasonal and shock load changes
• Final settlement performance and sludge return capability
• Space, energy and control-system constraints for future expansion

If you are comparing upgrade routes, Start the Engineering Assessment to check the likely treatment sequence against current and future compliance needs.

How this applies to your plant

If your plant is under review, the first question is not whether you need a new piece of equipment. It is which treatment stage is limiting compliance now, and which stage will become limiting next.

Use this practical sequence:

1. Confirm the agglomeration size in p.e. and compare it with the directive thresholds.
2. Check whether your current plant provides genuine secondary biological treatment, not only primary clarification.
3. Compare current effluent performance with the Annex I secondary-treatment standards for BOD5, COD and TSS.
4. Identify whether the receiving water or agglomeration is likely to trigger tertiary nutrient-removal requirements later.
5. Review whether existing primary, secondary and settlement assets have enough spare capacity to support upgrade options.

The main point is simple: primary treatment prepares the load, secondary treatment removes biodegradable pollution, and tertiary treatment addresses nutrients and polishing where required. For EU compliance, the biological stage is central, but it should always be assessed as part of the whole treatment train rather than in isolation.

If you are planning an upgrade, the best starting point is a process and capacity review. Start the Engineering Assessment to evaluate how your current plant aligns with the directive and what treatment stages are likely to be needed next.