Learn More: Bacteria

What does this mean?

Bacteria are everywhere, including in our surface waters. Most are harmless. Water resource managers test for the presence of certain bacteria in waterways to protect human health. Some kinds of bacteria may cause illness if people are exposed to them, and others are harmless but their presence may indicate contamination from sources that may contain other, harmful pathogens. The presence of bacteria can affect our ability to use surface water for drinking, swimming, and shellfish production and harvesting.

Bacteria come from a variety of sources, but those of most concern for human health come from the fecal waste of animals and people. Sources of fecal bacteria include:

  • Malfunctioning septic systems
  • Leaking sanitary sewers
  • Confined animal feedlots / overgrazing
  • Wastewater plant overflows
  • Urban pet waste
  • Wildlife

Water quality regulations identify the specific type(s) of bacteria used to indicate contamination from sources that may contain harmful pathogens.

  • Enterococci typically are not considered harmful to humans but their presence in the environment may mean that the water is contaminated by fecal material and that other disease-causing agents such as viruses, bacteria, and protozoa also may be present. Enterococci are distinguished by their ability to survive in salt water and thus they are the preferred indicator of health risk in estuarine and marine environments.
  • Fecal coliform bacteria are able to grow in elevated temperatures and are associated only with fecal material from humans and other mammals. While most are harmless the most common one, Escherichia coli (often abbreviated E. coli), can cause intestinal illness if ingested.

The maximum allowed number of these specific type(s) of bacteria in a waterway depend on the “designated use” of the waterway. Each waterway is assigned a “Class” which indicates how it is used by people.

The state water quality standards establish bacteria limits for each class.

  • Class I waterways are sources of potable water, like reservoirs. Water quality standards require that they be tested for E. coli. Water drawn from Class I waters is treated to kill bacteria prior to distribution as potable water.
  • Class II waters are used for shellfish propagation or harvesting. Water quality standards require that they be tested for fecal coliform bacteria (E. coli is one of these). In addition, the Florida Department of Environmental Protection (FDEP) uses the Florida Dept. of Agriculture and Consumer Services (FDACS) current open/closed shellfish harvest status report to determine impairment at the time of assessment, and any Class 2 waters that include "Prohibited" shellfish harvesting areas are deemed impaired for fecal coliform. ("SEAS Classification" is the stated reason for impairment). The FDACS water quality data itself is not included in the assessment and therefore, there may be waterbodies that are shown to be impaired for fecal coliform (SEAS Classification), although there are no data for fecal coliform available on the Water Atlas. For more information about shellfish assessment, refer to this document.
  • Class III and Class III Limited* waters are used for recreation. Most waterways in Florida are Class III. For Class III waters, different bacteria rules apply for freshwater and saltwater. “Predominantly fresh” waters must meet water quality standards for E. coli, and “predominantly marine” waters must meet standards for Enterococci.

*Class III-Limited waters are similar to Class III, but have special water quality rule(s) applied to them because of exceptional environmental circumstances. These “Site Specific Alternative Criteria” are defined in Rule 62-302.800 of the Florida Administrative Code).

In addition to performing bacteriological testing required by the water quality standards, some water resource managers may test for other bacteria as well. These tests, and tests of other water quality characteristics, help in identifying possible source(s) of contamination.

How are the data collected? (Methods)

Samples are collected in sterile 100-milliliter (ml) containers and transported to a certified laboratory. The samples must be kept cool during transit. During sample collection, environmental conditions are also observed and recorded, along with recent rainfall amounts.

Historically, sample analysis involved filtering water samples to isolate targeted bacteria types, incubating the result, and counting bacteria colonies. Newer methods use chemical analysis to detect metabolized enzymes produced by targeted bacteria to detect their presence and estimate their abundance. These methods are more economical, take less time, and are less subjective than the earlier methods.

Analysis results are reported as “Colony Forming Units (CFU)”, “Most Probable Number (MPN)” of colonies, or as “Membrane Filter (MF)”, which is equivalent to CFU. These units are functionally equivalent and refer to the number of bacteria cells present, or estimated to be present, in the sample.


Below is an excerpt from Rule 62-302.530 of the Florida Administrative Code, effective 2/17/2016, which defines water quality standards related to the maximum allowable level of each type of bacteria for each waterway class.

A geometric mean is the nth root of the product of n values:

geometric mean formula

A geometric mean minimizes the effect of very high or very low values, which would bias the result if a straight average (arithmetic mean) were used.


Water Quality Standard

(Potable water)

Escherichia coli

Counts shall not exceed a monthly geometric mean of 126 nor exceed the Ten Percent Threshold Value (TPTV) of 410 in 10% or more of the samples during any 30-day period. Monthly geometric means shall be based on a minimum of 5 samples taken over a 30-day period.

(Shellfish production and harvesting)

Fecal Coliform

Counts shall not exceed a median value of 14 with not more than 10% of the samples exceeding the Ten Percent Threshold Value (TPTV) of 43 (for MPN) or 31 (for MF), nor exceed 800 on any one day. To determine the percentage of samples exceeding the criteria when there are both MPN and MF samples for a waterbody, the percent shall be calculated as 100*(nmpn+nmf)/N, where nmpn is the number of MPN samples greater than 43, nmf  is the number of MF samples greater than 31, and N is the total number of MPN and MF samples.

For shellfish areas to be classified Approved or Conditionally Approved, the level of fecal coliform in subsurface water samples must meet the NSSP 14/31 standard. This standard is a geometric mean of at least 30 samples not to exceed 14 colony forming units (CFU) per 100 milliliters (ml) of water. A second part of this standard addresses the variability of the data and requires that the 90th percentile not exceed 31 CFU/100 ml (10% of the samples cannot exceed 31 CU/100ml).

Prior to August 2012, Fecal coliform was measured using most probable number (MPN/100ml) using 5-Tube Dilution. After August 2012, Fecal coliform is measured using colony forming units (CFU/100ml) using Mtec (Direct plating).

III and III-Limited, Freshwater


Escherichia coli

MPN or MF counts shall not exceed a monthly geometric mean of 126 nor exceed the Ten Percent Threshold Value (TPTV) of 410 in 10% or more of the samples during any 30-day period. Monthly geometric means shall be based on a minimum of 10 samples taken over a 30-day period.

III and III-Limited, Marine



MPN or MF counts shall not exceed a monthly geometric mean of 35 nor exceed the Ten Percent Threshold Value (TPTV) of 130 in 10% or more of the samples during any 30-day period.  Monthly geometric means shall be based on a minimum of 10 samples taken over a 30-day period.

The water quality standards above are excerpted from regulations in the Florida Administrative Code.

Advisory standards that protect health and safety are also important. The Florida Healthy Beaches program is administered by the Florida Department of Health and its county health departments. It protects beachgoers from conditions unsuitable for swimming by sampling beach water and providing accurate and up-to-date explanations of the results. Sampling is performed biweekly to detect Enterococcus bacteria, which can come from a variety of natural and human-made sources. Sample results are summarized and posted on the Florida Department of Health website. Results are categorized at "Good", "Moderate", or "Poor", based on the quantity of bacteria found in a 100-milliliter sample:

  • Good: 0–35.4 cells/mL
  • Moderate: 35.5–70.4 cells/mL
  • Poor: 70.5 or more cells/mL

A "Poor" rating may result in a resampling event to confirm poor conditions, and the Florida Dept. of Health may choose to issue a Health Advisory or Warning immediately. These indicate that contact with the water at the site may pose increased risk of infectious disease, particularly for susceptible individuals.

Caveats and Limitations

Environmental contamination can be very localized or patchy, especially if the source of contamination is wildlife. Bacteria may persist in a waterbody for a period after its source is eliminated. Poor sample results may reflect the immediate area where sampling occurred, but not necessarily be representative of water quality in the entire water body. Conversely, while waters with indicators exceeding the levels in water quality standards may be considered a potential health risk, that does not mean that levels within acceptable ranges are entirely free of risk.