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Part II: Section E: Microbiological Guidelines for Freshwaters

The framework in these guidelines uses both beach grading and guideline values. Beach grades provide the basic means to assess suitability for recreation over time, using a combination of knowledge of beach catchment characteristics and microbiological information gathered over previous years. Single-sample results are compared against guideline values, to help water managers determine when management intervention is required. The guideline values that have been decided on are summarised in E.5.

Throughout this document the term ‘beach’ refers to both marine and freshwater recreational water sites.

E.1 Designation of a contact recreation area

People are generally free to swim wherever they like around New Zealand’s many beaches, but it would be impossible to monitor them all. Criteria for identifying which beaches to monitor will vary from region to region, but will generally be based on usage, available information and the resources available to the monitoring authority. The Ministry for the Environment and Ministry of Health recommend that the beaches to be included in the monitoring programme be agreed by all agencies involved in the programme and documented in the regional protocol.

E.2 Sampling rivers and lakes

The following information is provided to help develop a sampling programme for monitoring rivers and beaches.

Sampling period

Samples should be collected during the bathing season, or when the water body is used for contact recreation. For rivers this may exclude periods of high flow, during which hazardous river conditions would prohibit bathing. The bathing season will vary according to location, but will generally extend from 1 November to 31 March. Sampling should take place between 8 am and 6 pm.

See Note H(i) for details on sampling times and periods.

Bacteriological indicators, catchment assessment and single samples

The pathogens occurring in contaminated freshwater are the same as those occurring in marine waters, except that survival times in freshwater are likely to be longer, especially for protozoan cysts (e.g. Giardia and Cryptosporidium) and viruses. E. coli is the preferred indicator organism for freshwaters, although there may be exceptions (e.g. in proximity to large waste stabilisation pond outfalls). Enterococci should not be used because some enterococci can multiply from natural sources, such as the decay of leaf material. This means that enterococci levels can be very high even in pristine waters, but this may not necessarily indicate high levels of pathogens.

Type of sampling programme

The guidelines recommend a systematic random-sampling regime. Generally this means samples should be collected weekly, regardless of the weather. There may be exceptions if conditions present a health and safety hazard, in which case samples should be collected as soon after the programmed time as possible.

Sampling depth

Samples should be taken at approximately 30 cm below the surface, where the depth of the water is approximately 1 metre.

See note H(ii) for techniques for taking and analysing samples.

E.3 Grading a freshwater site

The results we obtain from microbiological sampling under a monitoring programme are only one aspect of the process. We also need to grade the site we are monitoring. There are two components to grading freshwater sites:

  • the Sanitary Inspection Category (SIC), which generates a measure of the susceptibility of a water body to faecal contamination
  • historical microbiological results, which generate a Microbiological Assessment Category (MAC). This provides a measurement of the actual water quality over time.

The two combined give an overall Suitability for Recreation Grade (SFRG), which describes the general condition of a site at any given time, based on both risk and indicator bacteria counts. The SIC, MAC and SFRG are explained below.

Note: Whereas before the guidelines were not applicable where a site received treated sewage, the grading system now allows an assessment of the health risk present at a site after evaluating the effectiveness of the treatment processes.

Assessing a freshwater site

The recreational water-quality decision tree (Figure E1) and accompanying descriptions outline the process that will lead to grading a site. All freshwater sites will have to go through this process, which helps to identify the information needed in order to grade a site.

Collecting background information

As much information as is feasible about the site should be collected to make the assessment of risk-contributing factors as accurate as possible. Sources of information will vary from region to region. Gathering this information may involve a range of agencies (health, water and sewerage industries; district, city, regional councils), which will have access to different information for the same site catchment. Relevant information includes drainage plans, site maps, previous season’s monitoring results, and consent applications. The purpose of the decision tree is to provide a logical course that allows the responsible authority to make defensible decisions on whether or not to grade a particular water body.

Figure E1: Recreational water-quality decision tree (duplicated)

The following notes describe the process and decisions required to complete each of the steps described in Figure E1.

Step 1: Is the water body used for contact recreation?

Beaches are considered either contact recreation areas (well used) or not contact recreation areas (not well used). The guidelines apply to contact recreation areas, and involve grading and monitoring.

This does not mean water quality can be allowed to deteriorate at ungraded beaches. Rather, it is expected that the guidelines will be rigorously applied at graded beaches, while the monitoring required and associated costs may not be justified at ungraded beaches.

Which beaches are monitored will be a local decision, and should be decided on a site-specific basis by the local authorities (regional or local authority, or Medical Officer of Health) depending on the local relevance of the site.

Step 2: Are catchment risk factors present?

The ‘risk factors’ refer to activities in the catchment that may result in faecal contamination of a recreational water site. To assess the catchment risk factors, the Catchment Assessment Checklist should be completed.

See Note H(vii) for the Catchment Assessment Checklist for freshwater recreational areas.

‘Yes’ responses to the ‘Microbiological Hazards’ (Part D) section of the checklist show the presence of catchment risk factors that affect, or are likely to affect, recreational water quality.

Step 3: Is there a wastewater treatment plant present?

Wastewater treatment processes often effectively reduce microbial indicators such as enterococci but are less effective at removing pathogens such as viruses. The result may be an altered pathogen-to-indicator ratio compared to that of untreated waste. This means that if there is a wastewater treatment plant present, pathogens may still be present even when indicator levels are very low.

See Note H(iii) for Catchment Assessment Checklist Base Conditions – discussion on risk assessment for tertiary treated effluent.

A ‘Yes’ answer in this box means the wastewater treatment plant discharges directly to the recreational water, or to an area where discharge water may reasonably be expected to be carried to a recreational water site by tides, currents or streams.

Step 4: Is there existing microbiological data?

Ideally there should be 100 data points [Data points are the results of samples collected.] or greater collected over the previous five years, although it is feasible to consider grading with a minimum of 20 data points collected over one full bathing season. The data should normally be E. coli. The grading should be considered as interim until five years of data have been collected.

Note: Follow-up samples from an alert or action mode response should not be included in the data used to generate an MAC (see Step 6). If using the software provided by the Ministry for the Environment to generate grades, follow-up samples should be manually removed from the dataset.

See Note H(xv) for information on the software available to analyse results.

Step 5: Can you collect microbiological data?

If microbiological data is required, the sampling programme should collect at least 20 data points over the period of greatest recreational use. This will normally be the summer bathing season, but may vary with the types of recreational activity most common in the area.

Step 6: Determining a grade

In order to grade a recreational water body, the authority must establish:

  • the Microbiological Assessment Category (MAC): an MAC category (ranging from A to D) is established from the existing or collected microbiological data; definitions for the different categories are given in Table E1.
  • the Sanitary Inspection Category (SIC): this category is either Very High, High, Moderate, Low or Very Low, and is determined for a specific water body by using the SIC flow chart.

See Note H(vii) for the Sanitary Inspection Category flow charts for rivers and lakes.

The information for using the flow chart should come from the Catchment Assessment Checklist (CAC), Part D, and may require further investigation to establish the principal source of contamination.

Determining a grade involves using both the MAC and the SIC (see Table E2: Suitability for Recreation Grade matrix). A grade is established on the basis of five years’ data. Thereafter recalculation of the grade may be done annually using the previous five years’ data.

Step 7: Modifying a grade

Modifying a beach grade is a management option, applicable when requirements in these guidelines have been met.

Beach grades may be modified where management interventions can be demonstrated to effectively discourage recreational use during occasional and predictable contamination events. The modified grade should reflect the water quality conditions the public are usually exposed to, and be verified by the Medical Officer of Health.

See Note H(xii) for more information on modifying beach grades.

Step 8: Reassessment

Reassess on a five-yearly basis, or sooner if significant change occurs. Such changes will be reflected in new information in parts A, B, C and D of the Catchment Assessment Checklist. Examples of significant change would be:

  • altered catchment characteristics or land use
  • significantly higher or lower microbiological indicator levels
  • major infrastructure works affecting water-quality parameters.

Beaches graded Very Good will almost always comply with the guideline values for recreation, and there are few sources of faecal contamination in the catchment. Consequently there is a low risk of illness from bathing. Beaches graded Very Poor are in catchments with significant sources of faecal contamination, and they rarely pass the guidelines. The risk of illness from bathing at these beaches is high, and swimming is not recommended. For the remaining beaches (Good, Fair and Poor) it is recommended that weekly monitoring be carried out during the bathing season. The public will be informed when guideline values are exceeded and swimming is not recommended.

The Microbiological Assessment Category

The following table lists the criteria that define the MAC, based on five years’ historical data.

Table E1: Microbiological Assessment Category (MAC) definitions
A Sample 95 percentile =<130 Escherichia coli per 100 mL
B Sample 95 percentile 131–260 Escherichia coli per 100 mL
C Sample 95 percentile 261–550 Escherichia coli per 100 mL
D Sample 95 percentile >550 Escherichia coli per 100 mL

Note: The Hazen method is used for calculating the 95 percentiles (It is important to note there are several ways to calculate percentiles. Each uses a different formula, generating different results. The Hazen method has been chosen for these guidelines, as it tends to be about the ‘middle’ of all the options.).

See Note H(viii) for more information on the Microbiological Assessment Category for freshwater recreational areas.

The Sanitary Inspection Category (SIC)

The SIC allows the principal microbiological contamination from faecal sources to be identified and assigns a category according to risk. This category is then combined with the Microbiological Assessment Category (MAC) to determine a Suitability for Recreation Grade for each site in the programme.

Sources of human faecal contamination identified by the SIC may, as a result of treatment, be considered of low public health risk. There may, however, still be cultural or aesthetic objections to such faecal contamination.

This category is either Very High, High, Moderate, Low or Very Low, and is found for a specific water body by use of the SIC flow chart. The information for using the flow chart should come from Part D of the Catchment Assessment Checklist (CAC) and may require further investigation to establish the principal source of contamination.

See Note H(iii) for detail on how to establish a Sanitary Inspection Category.

The Suitability for Recreation Grade

SFRGs are Very Good, Good, Fair, Poor and Very Poor. To find the appropriate grading for the recreational water body, locate the box in the Suitability for Recreation Grade table (Table E2) that coincides with both the MAC and SIC for the water body.

Table E2: Suitability for Recreation Grade for freshwater sites
Susceptibility to faecal influence Microbiological Assessment CategoryIndicator counts
(as percentiles – refer Table E1)
Exceptional circumstances ***
=< 130 E. coli/ 100 mL
131–260 E. coli/ 100 mL
261–550 E. coli/ 100 mL
>550 E. coli/ 100 mL
Sanitary Inspection Category: Very Low Very Good Very Good Follow Up** Follow Up**  
Sanitary Inspection Category: Low Very Good Good Fair Follow Up**
Sanitary Inspection Category: Moderate Follow Up* Good Fair Poor
Sanitary Inspection Category: High Follow Up* Follow Up* Poor Very Poor
Sanitary Inspection Category: Very High Follow Up* Follow Up* Follow Up* Very Poor
Exceptional circumstances  


Indicates unexpected results requiring investigation (reassess SIC and MAC).
Implies non-sewage sources of indicators, and this should be verified.
Exceptional circumstances: relate to known periods of higher risk for a graded beach, such as during a sewer rupture or an outbreak of a potentially waterborne pathogen in the community of the recreational area catchment. Under such circumstances a grading would not apply until the episode has abated.

(For example: if MAC = C and SIC = Moderate, then Suitability for Recreation Grade = Fair.)

See Note H(ix) for more information on the Suitability for Recreation Grade for freshwater recreational areas.

See Note H(xiii) for percentile guideline values for freshwater.

See Note H(xv) for information on software to use for grading beaches.

E.4 Monitored beaches: surveillance, alert and action modes

So far we have looked at deciding which beaches to grade, and how to monitor a beach by taking samples. Next we need to look at putting these together in a process to manage the different scenarios that may arise.

These guidelines propose a three-tier management framework based on bacteriological indicator values:

  1. surveillance – involves routine (e.g. weekly) sampling of bacteriological levels
  2. alert – requires investigation of the causes of the elevated levels and increased sampling to enable the risks to bathers to be more accurately assessed
  3. action – requires the local authority and health authorities to warn the public that the beach is considered unsuitable for recreation.

Surveillance (routine monitoring)

Under the surveillance condition, beaches graded Good, Fair or Poor have the potential to be affected by faecal contamination events, and routine monitoring (e.g. weekly sampling) must continue (see Box 2). Guidance on when and where to sample can be found in section E.2, with further information in Note H(i).

Alert (amber) mode: single samples

The alert mode is triggered when a single bacteriological sample exceeds a predetermined value. Under alert mode, sampling frequency should be increased to daily, and catchment assessment data referred to for potential faecal sources. A sanitary survey should then be undertaken to positively identify the sources of contamination and the potential management options.

See Note H(vii) for the Sanitary Inspection Category flow charts for rivers and lakes.

Action (red) mode: consecutive samples

The action mode is triggered when a single sample exceeds a pre-determined value (see Box 2 for guideline values). Under the action mode, the local authority and health authorities warn the public, using appropriate methods, that the beach is unsuitable for recreation and arrange for the local authority to erect signs at the beach warning the public of a health danger.

See Note H(i) for discussion on sampling requirements.

See Note H(xvi) for information on reporting to the public.

See Note H(xvii) for management responses to exceedances.

E.5 Freshwater surveillance, alert and action levels

The surveillance, alert and action levels are summarised in Box 2. They are based on an estimate that approximately 5% of Campylobacter infections could be attributable to freshwater contact recreation.

See Appendix 2 for details on how guideline values have been developed.

Box 2: Surveillance, alert and action levels for freshwater
Acceptable/Green Mode: No single sample greater than 260 E. coli/100 mL.
  • Continue routine (e.g. weekly) monitoring.
Alert/Amber Mode: Single sample greater than 260 E. coli/100 mL.
  • Increase sampling to daily (initial samples will be used to confirm if a problem exists).
  • Consult the CAC to assist in identifying possible location of sources of faecal contamination.
  • Undertake a sanitary survey, and report on sources of contamination.
Action/Red Mode: Single sample greater than 550 E. coli/100 mL.
  • Increase sampling to daily (initial samples will be used to confirm if a problem exists).
  • Consult the CAC to assist in identifying possible location of sources of faecal contamination.
  • Undertake a sanitary survey, and report on sources of contamination.
  • Erect warning signs.
  • Inform public through the media that a public health problem exists.


  • Colilert™ is the method of choice to enumerate E. coli or EPA Method 1103.1, 1985 Membrane Filter Method for E. coli (this method gives a result for E. coli within 24 hours): USEPA ICR Microbial Laboratory Manual.* This method and the MPN Method for E. coli, which is also acceptable (but gives a result in 48 hours), is described in the 20th edition of Standard Methods for the Examination of Water and Waste Water, American Public Health Association. These methods must be used to enumerate E. coli unless an alternative method is validated to give equivalent results for the waters being tested.
  • Samples to test compliance should be over the bathing season appropriate to that locality (at least 1 November to 31 March) and sampling times should be restricted to between 0800 hours and 1800 hours.

* USEPA National Centre for Environmental Publications and Information (NCEPI), 11029 Kenwood Road, Cincinnati, OH 45242, USA (Document No. EPA?821-C-97-004).

E.6 Conditions of using the guidelines

Use of these guidelines is conditional on the following.

  • These guidelines must not be used as a measure of suitability for recreation when there is a major outbreak of a potentially waterborne disease in the community, and that community’s sewage contributes to the microbiological contamination of the water. Such conditions constitute ‘exceptional circumstances’. The guidelines do not apply then because the relationship between indicator organisms and disease was derived when there were no known outbreaks of waterborne diseases in the community. When there is such an outbreak, health risks may be increased because of a higher-than-usual ratio of pathogen concentration to indicators in the water.
  • Implementing the guidelines emphasises the need and importance for traditional sanitary surveys.
  • Compliance with the guidelines generally indicates that a beach is suitable for recreation. There are exceptions however. For example, effluent may be treated to a level where the indicator bacterial levels are very low, but other pathogens such as viruses or protozoa may still be present at high levels. The assessment of such conditions should be considered during the procedure for grading a beach.
  • It is important that water managers use these guidelines judiciously, and carefully consider where they can be applied.

These guidelines are not intended to be used as the basis for establishing conditions for discharge consents, although they may be used as a component for decision making. See the Introduction of these guidelines for discussion on what this document covers.

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