A first order decay function is used to calculate changes in bacteria concentrations (Bowie et al., 1985).

$bact_{lprch,i}=bact_{lprch,i-1}*exp(-\mu_{lprch,die})$ 7:5.1.1

$bact_{prch,i}=bact_{prch,i-1}*exp(-\mu_{prch,die})$ 7:5.1.2

where $bact_{lprch,i}$ is the amount of less persistent bacteria present in the reach on day $i$ (#cfu/100mL), $bact_{lprch,i-1}$ is the amount of less persistent bacteria present in the reach on day $i-1$ (#cfu/100mL), $\mu_{lprch,die}$ is the rate constant for die-off of less persistent bacteria in streams (1/day), $bact_{prch,i}$ is the amount of persistent bacteria present in the reach on day $i$ (#cfu/100mL), $bact_{prch,i-1}$ is the amount of persistent bacteria present in the reach on day $i-1$ (#cfu/100mL), and $\mu_{prch,die}$ is the rate constant for die-off of persistent bacteria in streams (1/day).

The die-off rate constants are adjusted for temperature using the equations:​

7:5.1.3

7:5.1.4

where , is the rate constant for die-off of less persistent bacteria in streams (1/day), is the rate constant for die-off of persistent bacteria in streams (1/day), is the rate constant for die-off of less persistent bacteria in streams at 20C (1/day), is the rate constant for die-off of persistent bacteria in streams at 20C (1/day), is the temperature adjustment factor for bacteria die-off/re-growth, and is the water temperature (C).

Table 7:5-1: SWAT+ input variables that pertain to bacteria die-off in the stream.

In sediment channel routing, the maximum concentration of sediment that can be transported by the water, $conc_{sed,ch,mx}$, (ton/m$^3$ or kg/L) is compared to the concentration of sediment in the reach at the beginning of the time step, $conc_{sed,ch,i}$ (Neitsch et al., 2005).

If $conc_{sed,ch,i}$ < $conc_{sed,ch,mx}$, resuspension is the dominant process in the reach segment and the net amount of sediment reentrained is calculated:

$sed_{deg}=(conc_{sed,ch,mx}-conc_{sed,ch,i})*V_{ch}*K_{ch}*C_{ch}$ 7:5.2.1

where $sed_{deg}$ is the amount of sediment reentrained in the reach segment (metric tons), $conc_{sed,ch,mx}$ is the maximum concentration of sediment that can be transported by the water (ton sediment/m$^3$ H$_2$O or kg sediment/L H$_2$O), $conc_{sed,ch,i}$ is the initial sediment concentration in the reach (ton sediment/m$^3$ HO or kg sediment/L HO), is the volume of water in the reach segment (m HO), is the channel erodibility factor (cm/hr/Pa), and is the channel cover factor. When sediment resuspends, both bacteria in sediment solution and on sediment particles are released, and the net amount of bacteria released from streambed is calculated:

7:5.2.2

where is the amount of bacteria released from streambed in the reach segment (# cfu), is the amount of sediment reentrained in the reach segment (metric tons), and is the concentration of bacteria in streambed in the reach segment (# cfu/ton sediment). Bacteria concentration in streambed is calculated by the empirical regression equation, logarithmic sine function of the days of year:

7:5.2.3

where is the concentration of bacteria in streambed (# cfu/ton sediment), day is the days of year, and through are the regression coefficients in streambed bacteria concentration equation.

If > , deposition is the dominant process in the reach segment and the net amount of sediment deposited is calculated:

7:5.2.4

where is the amount of sediment deposited in the reach segment (metric tons), is the initial sediment concentration in the reach (ton sediment/m HO or kg sediment/L HO), is the maximum concentration of sediment that can be transported by the water (ton sediment/m HO or kg sediment/L HO), and is the volume of water in the reach segment (m HO). When suspended sediment deposits, bacteria on settling sediment particles are deposited, and the net amount of bacteria settled from stream water is calculated (Bai and Lung, 2005):

7:5.2.5

where is the amount of bacteria settled from stream water in the reach segment (# cfu), is the amount of bacteria in the stream water in the reach segment at the beginning of the time period (# cfu), is the linear partitioning coefficient of bacteria between the suspended sediment and water (m HO/ton sediment or L HO/kg sediment), is the amount of sediment deposited in the reach segment (metric tons), is the volume of water in the reach segment (m HO), and is the initial sediment concentration in the reach (ton sediment/m HO or kg sediment/L HO). The linear partitioning coefficient is calculated from the empirical regression equation (Pachepsky et al., 2006):

7:5.2.6

where is the linear partitioning coefficient of bacteria onto the suspended sediment (m HO/ton sediment or L HO/kg sediment) and is the percentage of clay in suspended sediment in stream water in the reach segment (%). clay normally varies between 2 and 50%.

Once the amount of bacteria released and settled has been calculated, the final amount of sediment in the reach is determined:

7:5.2.7

where is the amount of bacteria in the stream water in the reach segment (# cfu), is the amount of bacteria in the stream water in the reach segment at the beginning of the time period (# cfu), is the amount of bacteria released from streambed in the reach segment (# cfu), and is the amount of bacteria settled from stream water in the reach segment (# cfu).

The final bacteria concentration in the reach is calculated:

7:5.2.8

where is the concentration of bacteria in the stream water in the reach segment (# cfu/100 mL), is the amount of bacteria in the stream water in the reach segment (# cfu), and is the volume of water in the reach segment (m HO).

SWAT+ calculates loading of pathogens and indicator bacteria for pathogens from land areas in the watershed. In the stream, bacteria die-off is the only process modeled.