Water Quality Monitoring

Monitoring stream flow


There are two parts of the permit that call for water quality monitoring. One requires wet weather monitoring of all outfalls that discharge directly to any stormwater impaired waters to determine what areas are contributing to the impairment. This requirement is detailed on pages 41-44 of the MS4 permit.

The other monitoring requirement is part of tracking down illicit discharges to the MS4 via the IDDE program. See pages 7-11 in Appendix B of the permit for details.

Relevant terms

Wet weather monitoring: means sampling an outfall during or after any rainfall event that results in a discharge from the outfall.

Dry weather monitoring: means sampling an outfall only when no more than 0.1 inches of rainfall has occurred in the previous 24 hours.

Stormwater impaired waters: means a subset of the surface waters of the state identifed as impaired in the most recent Connecticut Integrated Water Quality Report as a result of stormwater runoff. See the MS4 Map Viewer for a map layer of CT's stormwater impaired waterbodies.


Monitoring requirement comparison chart

This chart outlines the key elements of the two main monitoring requirements in the MS4 general pemit: Impaired waters monitoring and IDDE monitoring. IDDE monitoring requirements are split into two sections: Baseline monitoring and the Catchment Investigation Procedure.

Download [86 KB]

Impaired waters monitoring flowchart

Download [33 KB]

IDDE baseline monitoring flowchart

Download [29 KB]

IDDE catchment investigation procedure flowchart

Download [43 KB]

Sampling Cost Estimates

We compiled example monitoring equipment that may be used to meet permit requirements and included costs for both in-house test kit/portable meter sampling vs. laboratory services. We've also created a map of the certified labs towns can use to analyze samples for bacteria, total N and total P.

NOTE: Bacteria sampling can’t be done in the field so requires lab services.

Test kit/Meter vs Lab Cost Estimates
Pollutant Test Kit/Meter Price Samples per kit Cost per sample Comments Commercial lab cost per sample (estimate)
Ammonia Hach N1-8 $88 100 $0.88 Reagent for this kit contains mercury $9.00
Surfactants Hach DE-2 $307 32 $9.59   $16.00
Chlorine Hach CN-66F

Quantofix Chlorine test strips



Sampling for either free chlorine or total chlorine is acceptable. DEEP is looking for detectable chlorine and the test kits or strips should have a lower detection limit of 0.1 mg/l or less. $3.00
Turbidity Hach 2100Q $1180 n/a     TBD
  LaMotte 2020we $980 n/a      
  HF Scientific MicroTPW $799 n/a      
Nitrogen, phosphorus Lamotte Smart3 (Requires Heater Block for TN/TP) $999 + $779 (heater block) = $1778 $123 (TN)
$4.90 (TN)
$7.56 (TP)
  • Reagents also need to be purchased.
  • Samples need to be digested in heater block prior to analysis (can't be done in field)
  • Per sample costs do not include cost of meter and heater block
$8 (TP)
$23 (TN)

Impaired waters monitoring factsheet

Monitoring of stormwater outfalls is required under the new MS4 permit, however the approach is slightly different than under the 2004 permit.

Now, all MS4 outfalls that discharge directly to stormwater impaired waters should be sampled at least once during the 5-year term of the permit. Visit our MS4 Map viewer to find out what waters in your town are impaired by stormwater. Note that all MS4 outfalls must be inventoried and mapped as part of the IDDE requirements but for this requirement, those outfalls that discharge to stormwater impaired waters must also be sampled for that impairement.

If you already have wet weather sampling data, it can be used to meet this requirement.

Key instructions:
  • Only sample for the existing stormwater impairment(s) (e.g. nitrogen, phosphorus, bacteria). If impairment is 'Other pollutant of concern', sample for turbidity.
  • Collect samples during any rain event that results in a discharge from the outfall.
  • Complete drainage area investigations where screening indicates high pollutant levels (see table below) and implement BMPs to address the impairment. As an example, if a waterbody exceeds the nitrogen limit, target residents in the watershed for outreach on reducing nitrogen.
  • Once half of all impaired waters outfalls have been sampled, select 6 of the highest polluting outfalls for annual screening.

Pollutant of Concern Screening threshold


Total nitrogen > 2.5 mg/l


Total phosphorus > 0.3 mg/l


For discharges to Class AA, A, and B surface waters:
- E. coli > 235 col/100ml for swimming waters and > 410 col/100ml for all others
- Total coliform > 500 col/100ml

For discharges to Class SA and SB surface waters:
- Fecal coliform > 31 col/100ml for Class SA and > 260 col/100ml for Class SB
- Enterococci > 104 col/100ml for swimming areas and > 500 col/100ml for all others

Other pollutant of concern

Turbidity 5 NTU greater than instream sample just upstream of outfall

IDDE monitoring factsheet

Before you begin the dry weather sampling requirements in the IDDE section, each MS4 must develop an inventory of all outfalls in priority areas, sort those outfalls into 4 categories (problem, high priority, low priority, excluded), and rank all the outfalls in each category based on specific characteristics. See the IDDE implementation section of this website or Appendix B of the permit for more details. 

The IDDE section requires dry weather sampling of outfalls in priority areas that are classified as high or low priority (it does NOT need to be done for catchments in priority areas that are classified as problem or excluded outfalls). Dry and wet weather sampling is to be used as part of the follow-up investigations to help identify where an illicit discharge is coming from.

What to test for

All the dry and wet weather samples may be done with test kits or meters (except bacteria) and need to be analyzed for the constituents listed below. Proper sampling procedures need to be followed - for more information, there's a recording of the IDDE Dry weather screening and sampling presentation given at the IDDE workshop on the IDDE page. Also, see EPA's guide to proper sampling procedures.

  • ammonia
  • chlorine
  • conductivity
  • salinity
  • E. coli. (freshwater) or enterococcus (saline or brackish receiving water)
  • surfactants
  • temperature
  • Pollutant(s) identified as causing the impairment of the receiving water, if it is impaired*

*Note that no test kits exist for total nitrogen or total phosphorus - these samples will likely need to be sent to a laboratory.

Samples that exceed any of the following criteria shall be ranked at the top of the High Priority catchments for further investigation:

  • Ammonia > 0.5 mg/L
  • Surfactants > 0.25 mg/L
  • Bacteria levels greater than the criteria applicable to the receiving water (see table on Impaired waters monitoring factsheet) OR detectable levels of chlorine.

Fieldwork checklist and data collection

Example spreadsheet for collecting required data during water quality sampling.

And an example fieldwork checklist used for water quality monitoring at the UConn Storrs campus.

Download [5.1 MB]

Task list

Most requirements for this section are in effect as of July 1, 2017 for all MS4s but more time is provided for the legal authority component.
Where the deadline for new MS4 permittees differs from the deadline for exisiting permittees, the second deadline in parenthesis applies to new permittees.

Activity Deadline Permit Page

Impaired Waters Monitoring

Complete inventory of all outfalls that discharge to impaired waters

Jul 1 2019
(Jul 1 2020)

Begin screening outfalls to impaired waters

Jul 1 2018
(Jul 1 2019)


Complete screening 50% of outfalls to impaired waters

Jul 1 2020
(Jul 1 2021)

Complete screening all outfalls to impaired waters

Jul 1 2022


Begin follow-up investigations where needed

Jul 1 2019
(Jul 1 2020)


Begin to monitor 6 'worst' outfalls annually

Jul 1 2020
(Jul 1 2021)


IDDE Monitoring

Complete dry weather sampling (of all MS4 outfalls in High & Low priority catchments)

Jul 1 2020
(Jul 1 2022)

Appendix B p.12

Conduct wet weather sampling where required as part of Catchment Investigation Procedure

No specific deadline

Appendix B p.10

Monitoring Workshop Materials

The NEMO program presented a workshop on the CT MS4 water quality monitoring requirements on June 20, 2019 at Milford City Hall. Most of the presentations were recorded. The presentation slides and recordings (where available) can be found below.

Overview of MS4 Monitoring Requirements, presented by Amanda Ryan, UConn CLEAR

MS4 Monitoring "DIY", presented by Mike Dietz, UConn CLEAR

Managing MS4 Monitoring for Large Municipalities, presented by Correne Auer, HRP Associates

Water Quality Monitoring Challenges and Data Management Solutions, presented by Joseph Canas and Sarah Bounty, Tighe & Bond

Partnerships in Water Quality Monitoring, presented by Carol Haskins, Pomperaug River Watershed Coalition