MSU Center for Water Sciences


Using qPCR to Assess Recreational Water Quality

Quantitative polymerase chain reaction (qPCR) methods can provide faster results than the current culture-based method for monitoring beaches. However, qPCR methods are relatively new- EPA released new criteria based on qPCR in 2012- and require specific equipment and expertise. Because implementing a new method can be challenging, we have developed guidance to help those new to qPCR through the process. Check out the site to learn more- you can jump straight to a section by clicking one of the below links:

qPCR Manual

Training Video

Resources and Links

Technical Assistance


qPCR Manual

This manual aims to provide technical assistance to laboratories that will be using qPCR for the first time. The content describes the steps necessary to decide whether qPCR is feasible, to outfit a qPCR laboratory, to collect and process samples, to apply quantitative polymerase chain reaction method for the detection of enterococci in recreational waters (Method 1611), and to interpret and report results.

The manual and individual chapters are pdf files. You will need Adobe Reader to view the files- click here to get Adobe Reader if you don't already have it.


Download entire manual:

A Guidance Document for Testing Recreational Waters Using EPA qPCR Method 1611

A. Aslan, J. Kinzelman, E. Dreelin, T. Anan'eva, and J. Lavender

Download individual chapters:

Chapter 1  Introduction

Chapter 2  Can I Use qPCR for Recreational Water Quality Monitoring?

Chapter 3  Setting up a qPCR Laboratory

Chapter 4  Pre-analytical Set Up for Method 1611

Chapter 5  Sampling for Recreational Water Quality Monitoring

Chapter 6  Analytical Procedures for Method 1611

Chapter 7  Data Assessment

Chapter 8  Conclusion

Chapter 9  Strategies for Saving Time During qPCR Analysis

Glossary and References

Updated manual for E. coli Method C!
We have updated the manual for E. coli testing using EPA Method C. Click here for a pdf of the entire updated manual.


Training Video

See qPCR in action. This video will lead you through the qPCR analysis step-by-step.

Click here to watch the video

Dr. Asli Aslan provided the technical expertise to develop this training video. Dr. Amol Pavangadkar produced and directed the video with his team in Communication Arts & Sciences.


Resources & Links

Methods and Criteria

EPA Method 1611 (pdf)

EPA Recreational Water Quality Criteria Website


Training Opportunities

No organized training sessions currently scheduled.


Are you a Michigan lab setting up qPCR? MSU offers training sessions at MSU and visits to your lab. Contact Dr. Tiong Gim Aw to schedule a session.

Training Videos

qPCR in Your Lab Video, Water Environment Research Foundation

Southern California Coastal Water Research Project qPCR training video

University of Liverpool PCR video

SimpleScience Introduction to PCR video

Ask TaqMan Video Gallery, Life Technologies Corporation

MIqPCR Listserv

The goal of MIqPCR listserv is to provide a forum for those in Michigan using qPCR for monitoring water. To be added to the listserv, contact Dr. Erin Dreelin.


Technical Assistance

Still have questions? We can help! Contact Dr. Tiong Gim Aw with questions about the qPCR method or setting up a qPCR lab.



This project is currently funded by the Michigan Department of Environmental Quality. Production of the manual and training video was funded by an EPA Great Lakes Restoration Initiative grant to the Michigan Department of Environmental Quality.


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