Secondary vs Tertiary Treatment: Key Differences

Introduction

Secondary and tertiary treatment are not interchangeable terms. In wastewater engineering, they refer to different objectives, different process stages, and different compliance drivers.

Secondary treatment is the biological stage that removes biodegradable organic matter from wastewater. Tertiary treatment is an additional polishing stage, usually introduced to remove nutrients such as nitrogen and phosphorus where the receiving water or regulation requires it.

For operators and designers, the distinction matters because it affects process selection, tankage, aeration demand, sludge production, resilience to load variation, and the level of compliance monitoring needed. It also matters under the EU Urban Wastewater Treatment Directive recast in Directive (EU) 2024/3019, which sets out a staged pathway for secondary, tertiary and quaternary treatment.

What secondary treatment does

Secondary treatment is the core biological treatment stage in an urban wastewater treatment works. The recast Directive defines it generally as biological treatment with a secondary settlement stage, or another process that removes biodegradable organic matter.

In practical terms, secondary treatment is designed to:

• oxidise dissolved and colloidal biodegradable organics;
• reduce biochemical oxygen demand (BOD5);
• lower chemical oxygen demand (COD) associated with biodegradable fractions;
• produce a settleable biological floc or biomass that can be separated from the treated water.

Common process families include activated sludge, oxidation ditches, trickling filters, and other biological systems that achieve carbon removal. The exact configuration varies, but the treatment objective is consistent: remove the biodegradable organic load before discharge.

The directive’s Annex I sets secondary-treatment effluent standards of:

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

These are treatment-stage compliance values for the biological process train. They do not describe nutrient removal performance.

Typical operational considerations

Secondary treatment performance depends strongly on process control and loading stability. Typical design and operating values are site-specific, but operators commonly focus on:

• dissolved oxygen control in aeration basins;
• sludge age and biomass retention;
• mixed liquor suspended solids balance;
• return activated sludge flow;
• clarifier solids loading and sludge blanket control;
• shock load management and industrial contribution control.

The main question for secondary treatment is whether the plant can consistently remove biodegradable organic matter under normal and peak conditions. If it cannot, the issue is usually in process capacity, oxygen transfer, solids separation, hydraulics, or upstream variability.

What tertiary treatment adds

Tertiary treatment is an additional treatment stage beyond conventional secondary treatment. Its purpose is not primarily to remove biodegradable carbon, but to polish the effluent so that nutrients are reduced to tighter limits.

In the EU framework, tertiary treatment refers to nitrogen and phosphorus removal. This is relevant where the receiving water body is sensitive to eutrophication or where the plant size triggers a higher level of treatment.

Typical tertiary process options include:

• biological nutrient removal configurations within the activated sludge process;
• chemical phosphorus precipitation;
• filtration combined with nutrient control measures;
• nitrification and denitrification stages;
• other site-specific nutrient removal solutions.

Unlike secondary treatment, tertiary treatment is driven by the need to manage nutrient discharges rather than the basic removal of organic pollution.

Why tertiary treatment is needed

Nitrogen and phosphorus can stimulate algal growth and ecological imbalance in receiving waters. Where water bodies are at risk of eutrophication, secondary treatment alone may be insufficient even if it meets BOD5, COD and TSS standards.

Tertiary treatment therefore acts as a compliance and environmental protection layer. It is generally added after the biological carbon-removal stage, although in many plants nutrient removal is integrated into the biological process rather than added as a fully separate unit.

Secondary vs tertiary treatment: the practical difference

The simplest way to distinguish the two is by their treatment objective:

• Secondary treatment removes biodegradable organic matter.
• Tertiary treatment removes nutrients, especially nitrogen and phosphorus.

That difference affects the whole design basis.

In process terms

Secondary treatment typically answers:

• How do we remove carbon-based pollution?
• How do we stabilise the wastewater biologically?
• How do we meet BOD5, COD and TSS limits?

Tertiary treatment typically answers:

• How do we remove remaining nitrogen and phosphorus?
• How do we protect the receiving water from eutrophication?
• How do we meet tighter environmental permit conditions?

In plant layout terms

Secondary treatment usually includes:

• biological reactors;
• aeration equipment or natural aeration systems;
• secondary clarifiers or equivalent solids-separation units.

Tertiary treatment may add:

• additional anoxic or aerobic zones;
• chemical dosing points;
• filtration units;
• dedicated nutrient-removal infrastructure.

In operational terms

Secondary treatment is usually controlled around organic load removal and solids separation. Tertiary treatment is usually controlled around nutrient conversion and nutrient capture.

This distinction matters for energy use, chemicals, operator skill requirements, sludge handling, and process monitoring. A plant that can achieve secondary standards is not automatically capable of tertiary nutrient performance.

What the EU Directive requires

Directive (EU) 2024/3019, the recast Urban Wastewater Treatment Directive, sets the framework for treatment-stage obligations across the EU.

Key points relevant to this topic are:

• the directive entered into force on 1 January 2025;
• it 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 treatment stages:

• secondary treatment is mandatory for agglomerations of 2,000 p.e. and above;
• this obligation is extended 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;
• tertiary treatment is required for plants of 150,000 p.e. and above by 2039;
• tertiary treatment is also required for plants of 10,000 p.e. and above in areas at risk of eutrophication by 2045.

The directive also introduces quaternary treatment for micropollutant removal for larger works, but that is a separate stage from the secondary-versus-tertiary distinction.

Population equivalent in context

The directive defines a population equivalent as the organic biodegradable load having a five-day biochemical oxygen demand of 60 g of oxygen per day.

That definition is important because the thresholds above are based on p.e., not simply on headcount. A plant serving a relatively small population may still be hydraulically or organically significant depending on trade waste and infiltration effects.

How to decide whether a plant needs tertiary treatment

For existing plants, the question is not only whether secondary treatment is working, but whether future permit conditions or receiving-water constraints will require more than secondary treatment.

A practical engineering review should consider:

• current secondary effluent quality against permit requirements;
• evidence of eutrophication risk in the receiving water;
• current and forecast p.e. loading;
• available footprint for process upgrades;
• whether nutrient removal can be integrated into the existing biological process;
• sludge handling and dewatering implications;
• energy impacts, especially aeration demand;
• compliance timing under national transposition.

In some cases, optimisation of the existing secondary process is enough. In others, the plant needs a structured pathway towards nutrient removal, especially where growth or tighter environmental objectives are already visible.

If you are assessing upgrade options, it is often useful to start with a treatment-stage review of the works. You can Start the Engineering Assessment to check whether your current process is aligned with the likely compliance pathway.

Common misunderstandings

“Secondary treatment is the same as full treatment”

Not necessarily. Secondary treatment addresses biodegradable organic matter. It does not automatically deliver nutrient removal.

“If a plant meets BOD limits, it is future-proof”

Not necessarily. A plant can comply with secondary standards and still need tertiary treatment if nutrient limits are introduced or if the receiving water is sensitive.

“Tertiary treatment is always a separate building or unit”

Not always. In many plants, nutrient removal is incorporated into the biological process through zone configuration, internal recycles, or chemical addition.

“The directive applies the same way everywhere”

The EU framework is common, but transposition and implementation occur through national law, and transitional or exemption arrangements exist. Design decisions should therefore be checked against local permitting and implementation requirements.

How this applies to your plant

If your works is primarily designed for carbon removal, it is operating in the secondary-treatment space. If it must also control nitrogen and phosphorus to protect the receiving water or meet additional permit conditions, it is moving into tertiary treatment.

For plant owners and engineers, the key next step is to map three things together:

• current secondary performance;
• likely future nutrient obligations;
• physical and operational constraints at the works.

That combination determines whether the right response is optimisation, staged upgrading, or a full biological treatment upgrade. For a structured review of your treatment train and compliance pathway, use the Engineering Assessment and link it to the broader treatment-stage overview at [/treatment-stages].