CT is a measure of the strength of the disinfectant for the time that the water and disinfectant are in contact. CT is determined by multiplying the residual disinfectant concentration (C) by contact time (T). In order to calculate log inactivation for compliance with the surface water treatment rule the CT Achieved and CT Required must be calculated for each disinfection segment in your system.
Calculating CT Achieved For A Segment
EPA rules state  "Measurements must be taken on the same day of the week, every week, for one year (52 measurements), during peak hourly flow for that day. Data can be measured manually or with online instrumentation."
To meet EPA compliance you must calculate the CT Achieved for a day. There are 2 methods you can choose:
 Calc the CT Achieved for each hour and report the minimum.
 Calc the CT Achieved for the hour that the Peak Hourly Flow rate (for the segment) occurred.
In the examples below the following variables are used:
 V1: Hourly Flow Rate in MGD
 V100: Clearwell Water Depth (Ft.) Hourly Minimum
 V101: Clearwell Volume in MG
Method 1: Calculate CT Achieved for each hour:
1. Calculate segment volume in MG.
Based on current conditions (i.e. level in tank, number of filters on, etc…)
V101 = V100 * 28.27 * 7.48 / 1000000
 28.27 is CrossSectional Area of a 3 foot radius (Pi r2 = 3.14159 * 3^2)
 7.48 is number of gallons in 1 cubic foot
 1000000 is used to convert gallons to MG
2. Determine Baffling Factor (T10/T)
Baffling Condition 
T10/T 
Baffling Description 
Unbaffled (mixed flow) 
0.1 
None, agitated basin, very low length to width ratio, high inlet and outlet flow velocities. Can be approximately achieved in flash mix tank.
For a clearwell with no baffling you would use 0.1. 
Poor 
0.3 
Single or multiple unbaffled inlets and outlets, no intrabasin Baffles 
Average 
0.5 
Baffled inlet or outlet with some intrabasin baffles 
Superior 
0.7 
Perforated inlet baffle, serpentine or perforated intrabasin baffles, outlet weir or perforated launders 
Perfect (Plug Flow) 
1.0 
Very high length to width ratio (pipeline flow), perforated inlet, outlet, and intrabasin baffles 
3. Calculate T10 time in minutes
T10 = Detention Time (Mins) of Segment * Baffling Factor
= ((Segment Vol {MG} / Flow {MGD}) * 24 * 60) * Baffling Factor
V111 = (V101 / V1 * 24 * 60) * 0.3
4. Calculate CT Achieved
CT Achieved {mg/Lmins} = CL2 Residual {mg/L} * T10 {mins}
V115 = V141 * V111
Method 2: Calculate CT Achieved for Peak Hourly Flow Rate hour:
1. Calculate segment volume in MG.
Based on current conditions (i.e. level in tank, number of filters on, etc…)
V101 = DDWHEN(V100,V1,”MAX",V1,"",V1,"") * 28.27 * 7.48 / 1000000

DDWHEN(V100,V1,”MAX”,V1,"",V1,"") returns V100 for the hour when the Max Flow (V1) occurred.

28.27 is CrossSectional Area of a 3 foot radius (Pir2)

7.48 is number of gallons in 1 cubic foot

1000000 is used to convert gallons to MG
2. Determine Baffling Factor (T10/T)
Baffling Condition 
T10/T 
Baffling Description 
Unbaffled (mixed flow) 
0.1 
None, agitated basin, very low length to width ratio, high inlet and outlet flow velocities. Can be approximately achieved in flash mix tank.
For a clearwell with no baffling you would use 0.1. 
Poor 
0.3 
Single or multiple unbaffled inlets and outlets, no intrabasin Baffles 
Average 
0.5 
Baffled inlet or outlet with some intrabasin baffles 
Superior 
0.7 
Perforated inlet baffle, serpentine or perforated intrabasin baffles, outlet weir or perforated launders 
Perfect (Plug Flow) 
1.0 
Very high length to width ratio (pipeline flow), perforated inlet, outlet, and intrabasin baffles 
3. Calculate T10 time in minutes
T10 = Detention Time {Mins} of Segment * Baffling Factor
= ((Segment Vol {MG} / Flow {MGD} ) *24 * 60) * Baffling Factor
V111 = (V101 / DDMAX(V1,0,23) * 24 * 60) * 0.1
4. Calculate CT Achieved
CT Achieved {mg/Lmins} = CL2 Residual {mg/L} * T10 {Mins}
V115 = V141 * V111
Calculating CT Required for Segment
Determine which CT Required you need to calculate from the CT Tables provided in the EPA Guidance Manual Disinfection Profiling and Benchmarking

Determine if you need table for Giardi or Viruses removal

Determine the type of Disinfectant

Determine the Log Inactivation Required. Example, 3 log inactivation is required but the system may get "credits" for certain treatment techniques so they only need 1.5 log inactivation by disinfection.

Identify the variables for:

Water Temperature (Deg C)

pH

Disinfectant Residual

Example: Get CT Required for 2 log removal of Giardia by Free Chlorine
Using the Spread Function : CT(InactivationOf, Disinfectant, LogInactivation, Temp, pH, Cl2)
InactivationOf = "Giardia" or 1
Disinfectant = 1 for Free Chlorine
LogInactivation = 2
Temperature = V121 or in cell T10 in Spread Report
pH = V131 or in cell P10
Cl2 = V141 in cell C10
Spread Formula to Return CT is: CT(1,1,2,T10,P10,C10)
Math Toolbox formula is: V151 = CT(1,1,2,V121,V131,V141)
Calculate Segment Inactivation
1. Calculate the CT Ratio for 3 Log of Giardia and 4 log of Viruses.
CT Ratio = CT Achieved / CT Required
V161 = V115/V151
V165 = V115/V155
2. Calculate the CT Log Inactivation
Giardia Log Inactivation = 3 * CT Ratio
V171 = 3 * V161
Viruses Log Inactivation = 4 * CT Ratio
V175 = 4 * V165
Calculate the total Inactivation
We now must calculate the Segment Inactivation for all disinfection segments (steps). Then total the Inactivation for all segments to get the total Inactivation:
V901 = C171 + C271 +…
V905 = C175 + C275 + …
Other Methods to Calculate the CT Required which may match user's current method.
Use EPA Regression Equation
This method is calculated using regression equations developed by Smith et al. (1995). The equations can be found in Appendix E of USEPA Disinfection Profiling and Benchmarking Guidance Manual (EPA 815R99013), August 1999.
V151: CT Required  3 Log IA of Giardi
CT = (0.353*I)(12.006+e (2.460.073*temp+0.125*C+0.389*pH)) (for temperature < 12.5 °C)
CT = (0.361*I)(2.261+e (2.690.065*temp+0.111*C+0.361*pH)) (for temperature >= 12.5 °C)
Where:

I = 3, the number of logs inactivation required

Temp= temperature in degrees Celsius

C = residual chlorine concentration in mg/L

pH = the negative log concentration of hydrogen ion

e = 2.7183, the base for the natural logarithm
Therefore the Math Toolbox equation would be:
IF(V121<12.5,0.353*3*(12.006+EXP(2.46 .073*V121+0.125*V141+0.389*V131)), 0.361*3*(2.261+EXP(2.690.065*V121+0.111*V141+0.361*V131)))
Use CTR3LGC spread function or CTR3LGC Math Toolbox function
This is a method for approximating the CT Tables for 3 Log Inactivation of Giardia Cysts. The CT99.9 calculations for free chlorine use a complex interpolating polynomial which correctly reproduces virtually all of the CT table values for chlorine achieving a coefficient of correlation of .99999. Calculated values vary less than the instruments used to gather the data used in the calculations. The interpolating polynomial for calculating CT99.9 were developed by Russell J. Topham with the Utah Division of Drinking Water as part of his work with water treatment processes under the Surface Water Treatment Rule.
V151: CT Required for 3 Log IA of Giardi
=CTR3LGC (Disinfectant ID, Water Temperature, pH, Cl2 Residual)
=CTR3LGC(1, V121, V131, V141)
Disinfectant ID has one of the following settings:

Free Chlorine

Chlorine Dioxide

Chloramines

Ozone