Wastewater treatment using lagoons is widespread in certain areas. The lagoon treatment process usually works well for wastewater treatment in some regions, but the regulated lagoon effluent quality is not always met. The most frequent problems are elevated biochemical oxygen demand (BOD5), total suspended solids (TSS), ammonia (where regulated), and high or low pH. The odor from lagoons can also be troublesome.

Troubleshooting lagoons for effluent quality problems is not straightforward since the numerous biological and chemical processes involved are complex and not fully understood by some professionals, engineers and operators.

A biology- and chemistry-based approach to troubleshooting lagoon systems may help successfully correct lagoon
treatment problems.

Collection & interpretation

Lagoon effluent problems have many sources. The most common are: organic overloading and accompanying low dissolved oxygen conditions, short hydraulic detention time or short-circuiting, algae or sulfur bacteria overgrowth, old sludge accumulation, and partial nitrification.


High effluent BOD5 concentrations can point to many issues such as an incomplete wastewater treatment because of organic overloading, low oxygen concentration and low hydraulic detention time.


High effluent TSS is in many instances caused by high algae or sulfur bacteria growth.


High or low effluent pH problems can occur for different reasons. Low effluent pH of less than 7.0 may be caused by organic overloading or low oxygen conditions. High effluent pH is generally caused by extensive algae growth.


A major problem with ammonia removal in lagoons is the lower temperature of influent wastewater in the winter as a result of long hydraulic detention time.


Low oxygen conditions often cause odor in lagoons.

Lagoon effluent testing

Analysis tests for troubleshooting lagoon systems include:

  • Effluent BOD5 and TSS results for multiple years
  • Effluent carbonated BOD value
  • Effluent soluble BOD5 and total BOD milligrams per liter (mg/L)
  • Effluent pH variations
  • Lagoon dissolved oxygen fluctuations
  • Microscopic examination
  • Seasonal changes

Microscopic examination

Microscopic examination of the effluent using a phase contrast microscope can identify and quantitate specific organisms that cause effluent problems. The three most useful groups of indicator organisms are filamentous bacteria, algae and sulfur bacteria.

Filamentous bacteria are a large problem in activated sludge operation where their high growth causes sludge bulking.

Algae is a normal and needed biological component in a lagoon, responsible for much of the oxygen used in BOD stabilization even if the arrangement is mechanically aerated. However, these often overgrow and increase the effluent BOD5, TSS and pH.

A large presence of anaerobic sulfur bacteria in lagoon effluent indicates a significant anaerobic environment in the lagoon.

Microscopic examination of the effluent can also identify short-circuiting and sludge accumulation problems.

TSS to BOD5 ratio

Monitor the effluent’s TSS to BOD5 ratio for specific problems.

Organic overloading and low dissolved oxygen conditions

Organic overloading causes a low dissolved oxygen concentration of less than 1.0 mg/L and limits treatment. This condition can be evaluated by creating a dissolved oxygen profile for the entire lagoon.

Algae overgrowth

A microscopic test of the effluent and the enumeration of the algae present can determine if an algae overgrowth problem exists.


Short-circuiting is the passage of untreated wastewater through the lagoon system in a shortened period of time. This can happen because of poor mixing and the inappropriate location of lagoon inlet and effluent levels. Short-circuiting usually occurs in the winter when the incoming wastewater and lagoon temperatures differ significantly.

High effluent ammonia concentration

The high effluent ammonia concentration could be high at a cold temperature like 5°C because of the inhibition of nitrification at low temperatures. A high effluent ammonia concentration may also be caused by organic overloading, low oxygen concentration, short hydraulic detention time and the release of ammonia from old digesting sludge, most commonly in the late summer and fall at warm lagoon temperatures.

Partial nitrification

The effects of partial nitrification in a lagoon system can include ammonia and nitrifying bacteria in the effluent. Monitoring ammonia and nitrifying bacteria in the effluent can reveal partial nitrification issues.

Seasonal problems

Most of the lagoon problems that bear on the effluent quality occur seasonally, and the time of year the problem occurs can help disclose the cause.


Finding the cause of lagoon effluent problems is often a hard, perplexing challenge. The examples above yield ways to produce understandable and quantifiable information to pinpoint reasons for these issues.

Known in the industry as “Wastewater Dan,” Dan Theobald, proprietor of Environmental Services, is a professional wastewater and safety consultant/trainer. He has more than 24 years of hands-on industry experience operating many variants of wastewater treatment processing units and is anxious to share his knowledge with others.