What Happens During a Water Quality Test in a Lab?

For most people, water testing seems straightforward. You collect a sample from a faucet, well, tank, or other water source, place it in the correct container, and send it to a laboratory. After analysis, you receive a report showing what was detected and at what concentration.

But what actually happens to that sample once it reaches the laboratory?

Professional water analysis involves much more than simply placing water into a machine. Depending on the contaminants being investigated, laboratories may use microbiological methods, analytical chemistry, spectroscopy, chromatography, and other specialized techniques.

The exact procedure depends on:

The type of water
The contaminants being tested
The analytical method
Regulatory requirements
Sample preservation requirements
The intended use of the results

A professional water testing laboratory uses controlled procedures from sample receipt through analysis, quality control, data review, and final reporting.

This guide explains what typically happens during that process.

Step 1: Receiving, Logging, and Accessioning

The analytical process begins when the sample arrives at the laboratory.

Before testing starts, laboratory personnel review information associated with the sample.

This may include:

Customer information
Sampling location
Collection date and time
Requested analyses
Sample type
Preservation information
Chain-of-custody documentation when required

A typical workflow may look like this:

Sample Arrival → Documentation Review → Condition Check → Laboratory ID Assignment → Analytical Departments

Checking Sample Condition

Laboratory personnel may inspect:

Sample containers
Container seals
Sample volume
Preservation
Temperature, where applicable
Collection time
Holding-time requirements

Not every water test has the same preservation or temperature requirements.

Some analyses require refrigeration, while others may require:

Acid preservation
Specific containers
Protection from light
Immediate analysis
Other method-specific handling

EPA maintains information about approved drinking-water analytical methods, which illustrates why sample handling and analytical procedures must match the contaminant being evaluated.

Assigning a Laboratory Identification Number

Accepted samples are typically entered into a laboratory information-management system and assigned a unique identifier.

This helps laboratories track the sample through:

Preparation
Analysis
Quality control
Data review
Reporting

Tracking reduces the possibility of confusing one customer’s sample with another.

Step 2: Preparing Samples for Different Analyses

Water testing is not one universal procedure.

Testing for bacteria requires a completely different approach from testing for metals, nitrates, volatile organic compounds, or PFAS.

A laboratory may therefore prepare different portions of a sample for different analytical departments.

These portions are often called aliquots.

Microbiology Samples

Microbiological analysis requires procedures designed to minimize contamination introduced during collection or laboratory handling.

Depending on the method, samples may require:

Sterile containers
Specific holding times
Temperature control
Neutralization of disinfectants

Metals Samples

Samples being analyzed for metals may require acid preservation according to the analytical method.

The purpose is to maintain appropriate sample conditions before analysis.

Organic Chemistry Samples

Certain organic analyses may require:

Glass containers
Minimal headspace
Chemical preservatives
Protection from light

The exact container and preservation procedure depends on the compound and analytical method.

This is why homeowners and facility managers should follow the laboratory’s sampling instructions rather than collecting every sample in an ordinary household bottle.

Step 3: Microbiology Testing

When testing includes microbiological analysis, the sample is processed using a method appropriate to the organism or indicator being investigated.

Common drinking-water indicators include:

Total coliform bacteria
E. coli

EPA considers total coliform bacteria useful indicators for evaluating the adequacy of treatment and the integrity of drinking-water distribution systems.

More information is available through the EPA Revised Total Coliform Rule.

Different Microbiology Methods May Be Used

There is no single laboratory procedure used for every bacterial test.

Approved methods can include techniques such as:

Enzyme-substrate methods
Membrane filtration
Culture-based methods
Other validated procedures

EPA maintains microbiological analytical methods for water, including methods for detecting total coliforms and E. coli.

Enzyme-Substrate Testing

Certain approved methods use specialized nutrient substrates that react when target bacteria metabolize them.

Depending on the method, the laboratory may:

Add the required reagent to the sample
Incubate it under specified conditions
Examine the resulting reaction
Determine whether target organisms are present

Some methods use:

Color changes
Fluorescence under ultraviolet light
Quantitative well systems

However, the exact:

Temperature
Incubation time
Reagent
Interpretation criteria

depend on the specific approved method being used.

This is more accurate than assuming every coliform or E. coli test always follows exactly the same 24-hour procedure.

Specialized Legionella Testing

Legionella analysis is also different from routine total coliform or E. coli testing.

Legionella testing can require specialized:

Sampling
Sample processing
Culture methods
Laboratory interpretation

Facilities concerned about building water systems should first understand where Legionella can grow, including conditions involving warm water, stagnation, sediment, and biofilm.

Where appropriate, dedicated Legionella testing services can be incorporated into a broader building water-management or investigation program.

Legionella testing should not simply be treated as another routine household bacteria test.

Step 4: Testing for Metals With ICP-MS

Water samples requiring analysis for trace elements may be examined using highly sensitive analytical instruments.

One commonly used technology is Inductively Coupled Plasma Mass Spectrometry, or ICP-MS.

EPA Method 200.8 is an official analytical method for determining certain trace elements in water using ICP-MS. You can review the EPA Method 200.8 information.

Depending on the method and analysis, ICP-MS can be used for elements such as:

Arsenic
Lead
Cadmium
Copper
Chromium
Other trace elements

How ICP-MS Works

A simplified analytical sequence looks like this:

Liquid Sample → Nebulizer → Argon Plasma → Ion Formation → Mass Spectrometer → Detector → Concentration Result

Creating an Aerosol

The water sample is introduced into the instrument and converted into a fine aerosol.

Entering the Plasma

The aerosol enters extremely hot argon plasma.

The energy within the plasma converts elements in the sample into ions.

Separating the Ions

The ions then enter the mass spectrometer.

Different ions can be separated according to their mass-to-charge characteristics.

Measuring the Signal

A detector measures the resulting signals.

The instrument compares those signals with calibrated reference standards, allowing the laboratory to determine the concentration of individual elements.

Depending on:

Instrument
Method
Element
Sample matrix

very low concentrations can be measured.

Why Calibration Is Critical

An ICP-MS result is not generated simply by placing a water sample inside the machine.

Before and during analysis, laboratories use calibration and quality-control procedures.

These may include:

Calibration standards
Laboratory blanks
Continuing calibration checks
Matrix spikes
Duplicate samples
Reference materials

These controls help demonstrate that the analytical system is performing as expected.

Step 5: Testing Nitrates, Ions, and Other Chemicals

Not every contaminant can be measured with ICP-MS.

Other analytical technologies are used depending on the chemical being investigated.

Ion Chromatography

Ion chromatography, commonly called IC, can be used to analyze various dissolved ions.

Depending on the method, these may include:

Nitrate
Nitrite
Chloride
Fluoride
Sulfate
Other ions

A simplified workflow is:

Water Sample → Injection → Separation Column → Detector → Chromatogram → Concentration

The compounds are separated within the chromatography system before reaching a detector.

The resulting instrument response helps determine which compounds are present and their concentrations.

Gas Chromatography-Mass Spectrometry

GC-MS may be used for certain organic compounds and volatile contaminants.

Potential applications include analysis of:

Volatile organic compounds
Solvents
Fuel-related compounds
Certain industrial chemicals

The chromatography portion separates chemical compounds, while the mass spectrometer helps identify and measure them.

Other Laboratory Techniques

Depending on the requested parameters, laboratories may also use:

Spectrophotometry
ICP-OES
Atomic absorption spectroscopy
Liquid chromatography
Titration
Gravimetric methods
Electrochemical measurements

No single analytical instrument can measure every possible water contaminant.

Step 6: Measuring General Water-Quality Parameters

Some analyses focus on broader characteristics rather than individual contaminants.

These can include:

pH

Measures the acidic or alkaline condition of the water.

Conductivity

Provides information about the water’s ability to conduct electricity, which is influenced by dissolved ions.

Total Dissolved Solids

Provides an estimate or measurement of dissolved material depending on the method used.

Turbidity

Measures water cloudiness caused by suspended particles.

Hardness

Primarily reflects concentrations of calcium and magnesium.

Alkalinity

Measures the water’s ability to neutralize acids.

These parameters can help characterize overall water chemistry and guide decisions about additional testing.

Step 7: Quality-Control Review

Instrument output is not automatically released as a final laboratory result.

First, laboratory personnel review analytical quality-control information.

Quality-control procedures can include:

Blank samples
Calibration verification
Laboratory control samples
Spiked samples
Replicates or duplicates
Reference materials
Method-specific acceptance criteria

Why Blanks Matter

A blank is designed to contain little or none of the target contaminant.

If a contaminant unexpectedly appears in the blank, laboratory personnel may investigate whether contamination was introduced during:

Preparation
Reagents
Equipment
Analysis

Why Spikes Matter

A laboratory may add a known amount of a contaminant to a sample or control material.

The laboratory then evaluates how much of that known quantity is recovered.

This provides information about analytical performance.

Why Calibration Checks Matter

Analytical instruments can change slightly during operation.

Calibration checks help verify that the instrument remains within the method’s required performance limits throughout the analytical run.

Step 8: Data Validation

Once analysis is complete, laboratory staff review the data before issuing a report.

The review may include:

Instrument performance
Calibration
Quality-control results
Detection limits
Sample dilution
Unusual results
Method requirements

If quality-control criteria are not met, a laboratory may need to:

Reanalyze the sample
Dilute and rerun it
Reprepare it
Qualify the result
Request another sample

This validation stage is one reason professional laboratory testing provides more information than a simple home test strip.

Step 9: Comparing Results With Appropriate Standards

After laboratory results have been validated, they can be compared with an appropriate regulatory standard or health-based guideline.

For U.S. public drinking-water systems, EPA establishes legally enforceable requirements through the National Primary Drinking Water Regulations.

These regulations include Maximum Contaminant Levels, or MCLs, for many regulated contaminants.

An MCL is the highest permitted concentration of a regulated contaminant in drinking water under the applicable federal public-water-system requirements.

WHO Drinking-Water Guidelines

The World Health Organization’s drinking-water quality guidelines provide an important international scientific framework for drinking-water safety.

WHO guidance is widely used to support development of national standards and regulations.

However, WHO guidelines should not be confused with legally enforceable U.S. EPA regulations.

The benchmark used to interpret a laboratory result should reflect:

The country or jurisdiction
Type of water
Intended use
Applicable regulation
Specific contaminant

Step 10: Producing the Laboratory Report

After analytical and quality-control review, the laboratory prepares the final report.

A typical report may show:

Sample identification
Sample location
Collection information
Analysis performed
Contaminant name
Measured result
Measurement units
Reporting or detection limit
Analytical method
Result qualifiers
Other relevant notes

For example, a result might be reported in:

mg/L
µg/L
CFU per unit volume
MPN per unit volume

The units depend on the parameter and analytical method.

Understanding Detection Limits

A laboratory may report a result as:

Detected
Not detected
Below a reporting limit
Estimated

“Not detected” does not necessarily mean absolute zero.

It generally means that the substance was not detected above the laboratory’s applicable detection or reporting threshold under that method.

This distinction is important when interpreting laboratory reports.

Why Local Conditions Matter

Water chemistry and contamination risks can differ considerably between regions.

Relevant factors include:

Geology
Groundwater characteristics
Agriculture
Industry
Municipal infrastructure
Plumbing materials
Known contamination sites

The appropriate testing panel for one property may therefore be very different from another.

Property owners can review available water testing service locations when seeking laboratory support appropriate to their geographic area.

Local health departments and environmental agencies may also provide information about contaminants known to occur within a particular region.

Laboratory Testing vs. Home Testing Kits

Home test strips and portable meters can be useful for preliminary screening of certain basic parameters.

Depending on the product, these may include:

pH
Hardness
Chlorine
Nitrates
Other general measurements

However, laboratory analysis provides capabilities that basic home testing usually cannot match.

Professional analysis may provide:

Lower detection limits
Contaminant-specific methods
Quality-control documentation
Instrument calibration
Trace-level chemical analysis
Microbiological testing
Regulatory-grade data where applicable

A DIY kit may indicate that further investigation is warranted, but it should not be assumed to provide the same level of evidence as an appropriate laboratory method.

Why the Testing Process Varies

There is no universal workflow that every water sample follows.

A sample submitted only for:

pH
Hardness
TDS

may have a much simpler laboratory pathway than one submitted for:

PFAS
VOCs
Metals
Microbiology
Legionella

The professional water testing process therefore depends heavily on the requested analyses and purpose of testing.

For homeowners or facility managers unsure which analyses are necessary, the water testing FAQ provides additional information about sampling and laboratory testing.

Additional water-testing articles and resources can also help explain individual contaminants and analytical approaches.

From Sample to Scientific Data

The journey of a water sample can involve numerous steps:

Sample collection
Preservation
Transportation
Laboratory receipt
Accessioning
Sample preparation
Instrumental or microbiological analysis
Quality control
Data validation
Regulatory or guideline comparison
Final reporting

Every stage can influence the quality of the final result.

That is why accurate water testing begins before the sample enters an analytical instrument.

The Power of Professional Laboratory Analysis

Modern water laboratories can detect substances that are impossible to identify simply by looking at, smelling, or tasting water.

Depending on the contaminant, laboratories may use:

Microbiological culture
Enzyme-substrate methods
ICP-MS
ICP-OES
Ion chromatography
GC-MS
Spectrophotometry
Other specialized analytical techniques

EPA requires laboratories performing analyses for federal drinking-water compliance to use appropriate approved analytical methods, demonstrating how important standardized analytical procedures are to reliable regulatory data.

Laboratory analysis does not automatically prove that water is “perfectly pure,” and no single testing panel can detect every possible substance.

Instead, high-quality testing provides measurable scientific evidence about the contaminants and parameters included in the analysis.

That evidence can help homeowners, businesses, facility managers, and water professionals decide whether:

Additional testing is necessary
Treatment should be considered
Plumbing should be investigated
A contamination source requires attention
Follow-up monitoring is appropriate

If you need help deciding which analyses are appropriate for your water source, you can contact a professional water testing laboratory to discuss the property, water source, suspected contaminants, and purpose of testing.