Help Instruction File:

Bioreactor Module Overview

Provided by the Office of Surface Mining Reclamation and Enforcement (OSMRE), the Pennsylvania Department 

of Protection (PADEP), the U.S. Geological Survey's (USGS) and the West Virginia Department of Environmental 

Protection (WVDEP).
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Bioreactor Module Overview

Table of Contents

1.0 OBJECTIVE 5

2.0 TREATMENT COMPONENT OVERVIEW 5

2.1 Physical and Hydraulic Description 5

2.2 Application and Treatment Chemistry 6

2.3 Bioreactor Conceptual Treatment Model 7

2.3.1 Water Layer 7

2.3.2 Bio Mix Layer 8

2.3.3 Drainage Aggregate Layer: 9

2.3.4 Pipe Layer 9

2.3.5 Liner Layer 9

3.0 BIOREACTOR MODULE OVERVIEW 9

3.1 Layout and Workflow 9

3.2 Module Inputs 9

3.2.1 Water Quality and Flow Input 9

3.2.2 Sizing Methods 10

3.2.2.1 Sulfate Reduction 10

3.2.2.2 Alkalinity Generation Rate 10

3.2.2.3 Pilot Test Results 11

3.2.2.4 User-Specified Dimensions 11

3.2.2.5 Volumetric Calculations 11

3.2.2.6 Calculations for Sulfate Reduction, Alkalinity Generation Rate, and Pilot Test Sizing Methods 12

3.2.2.7 Calculations for User-Specified Dimensions Sizing Method 14

3.2.3 System Properties 15

3.2.4 Layer Materials 15

3.2.4.1 Freeboard Layer 16

3.2.4.2 Water Layer 16

3.2.4.3 Bio Mix Layer 16

3.2.4.5 Drainage Aggregate Layer 16

3.2.4.6 Pipe Layer 17

3.2.4.7 Liner Layer 17

3.2.5 Other Items 17

3.3 Module Outputs 17

3.3.1 Sizing Summary 17

3.3.2 Capital Cost 18

3.3.3 Annual Cost 18

3.3.4 Net Present Value 18
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3.3.4.1 Financial Variables 18

3.3.4.2 Cost Categories 18

3.3.4.3 Rationale for Recapitalization Recommendations 20

3.4 Assumptions of Design Sizing and Costs 21

4.0 REFERENCES 22

5.0 FIGURES 23

Figure 1: Typical Inverted Trapezoidal Prism 23

Figure 2: Typical Cross Section View of a Bioreactor showing the Common Layers and Components 23

Figure 3: Plan View of the Bioreactor to Illustrate Common Piping Layout and Components (Used in 

AMDTreat Piping Calculator) and the Layer Surface Areas. 24

Figure 4: Staging area for making the Bio Mix. Picture shows piles of manure, limestone fines, wood 

chips, and hay bales. 25

Figure 5: Large pile of Bio Mix (manure, compost, hay, woodchips, limestone) in preparation to be placed 

in Bioreactor. 25

Figure 6: Lateral piping network placed overtop of non-woven geotextile and synthetic liner. Note the 

pipes placed in rock bedding to protect perforated openings. 26

Figure 7: Close up image of effluent collection pipe embedded in rock shown in Figure 5. Image shows 

spur pipes (bottom left) connecting into the trunk (header) pipe (bottom right). 26

Figure 8. Excavator installing rock bedding for piping network. 27

Figure 9: Bioreactor under construction showing effluent collection pipe embedded in rock (bottom right) 

to be covered by Bio Mix layer. Pipe cleanouts were installed along the side slopes to remove debris if 

collection piping becomes clogged. Once a common practice, cleanout pipes are now sparingly used 

because of short circuiting issues experienced by flow along the sides of the clean out pipes. 28

Figure 10: Alternative piping network design. Spur pipes are aligned parallel to the longest dimension of 

the Bioreactor and the trunk (header) pipe is positioned across the width of the bioreactor. The piping 

network is embedded in stone to protect the perforations from the overlain Bio Mix layer. 29

Figure 11: Short term flush of a Bioreactor effluent pipe to prevent build up of precipitates. Whitish 

elemental sulfur flushed into a subsequent pond filled with ferrous monosulfide. FeS particulates 

constantly discharge from this bioreactor to the settling pond due to an insufficiently sized Bio Mix layer.

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Figure 12: Truck end-dumping the Bio Mix material and excavator trying to carefully smooth out the 

surface to obtain a uniform thickness to promote a uniform flow pattern. Extreme caution must be used to 

prevent compaction of the Bio Mix material, which is irreversible. 31
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Figure 13: Bio Mix being spread over top of a non-woven geotextile and synthetic liner system during the 

construction of a 2.0 acre Bioreactor. 32

Figure 14: Bioreactor filled with Bio Mix layer right before the initial filling with water and incubation 

period. Care was taken to create a uniform Bio Mix layer depth, however, the picture shows peaks and 

valleys within the Bio Mix that differ by up to a foot and will affect the flow pattern. Thus, this Bioreactor 

contains three separate piping systems (right side, middle, and left side of Bioreactor) that are controlled 

by three separate water control structures (e.g. Agri-drain boxes) to help equalize the uneven flow 

patterns caused by the variable thickness and homogeneity created during the construction. 33

Figure 15: Solubility of metal hydroxide vs. sulfides for various elements 34

Figure 16: Pourbaix diagram for an aqueous iron/sulfur system. Most mine drainage would plot within 

the SO4

2- stability field. The goal of a Bioreactor is to create an Eh/pH condition that plots in the pyrite 

stability field. 35

Figure 17: Monthly Influent and effluent sulfate concentration and effluent alkalinity concentrations for a 

Bioreactor over a five-year period. 36

Figure 18: Newly constructed Bioreactor being filled with mine drainage in preparation for a two-week 

incubation period. 37

Figure 19: First discharge of a newly constructed Bioreactor after the incubation period. The organic-rich 

water with elevated BOD & COD is an environmental concern if not appropriately treated in the 

subsequent ponds. 38

Figure 20: Discharge of a Bioreactor into the receiving stream right after the incubation period. Designers 

did not take proper precautions to treat the high BOD Bioreactor effluent water during the first few 

months of operation. 39

Figure 21: Photo showing a 3.0 by 3.0 ft area of the top of a Bio Mix layer under the water layer. One to 

two-inch diameter holes can be observed made by CO2 produced in the Bio Mix layer. The pH 2.7 mine 

water entering the Bioreactor and low pH iron oxidization is causing a ferric hydroxy sulfate mineral crust 

on top of the Bio Mix layer. 40

Figure 22: The milky-white water flowing out of a Bioreactor and through an outlet protection structure 

contains both elemental sulfur and calcite. 41

Figure 23: Black precipitate at the base of a bioreactor effluent pipe (black coated rocks to left of white 

pipe). Hydrogen peroxide is added to the black precipitate and the oxidation to produce an orange-red 

color ferric hydroxide confirms the precipitate as iron sulfide. 42

Figure 24: This photo is of the outfall from a Bioreactor effluent pipe. Note the black-colored pond in the 

background receiving this effluent. This Bioreactor contains an insufficient volume of Bio Mix layer 

needed to precipitate and settle the entire ferrous iron concentration and as a result ferrous sulfide (FeS) 

reactions continue to occur as the water is discharged from the Bioreactor. The Bioreactor discharges 

sixty (60) pounds of FeS as particulate matter every day, which is captured by the settling pond creating a 

potential environmental hazard in the form of stored acidity. To compound the seriousness of the iron 
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sulfide accumulation, a drinking water reservoir is shown at the very top of the photo that receives the 

final effluent from this Bioreactor treatment system. 43

Figure 25: While the photo is not a Bioreactor, the collection piping network shown here is the same 

configuration as the default piping in AMDTreat (if the AMDTreat Piping Calculator is used). A large 

trunk pipe extends along the center of the bottom length of the treatment component and spur pipes 

extend the width to collect and transport treated water out of the pond. The entire effluent piping network 

in a Bioreactor should be embedded in a drainage aggregate layer to protect the spur pipe perforations 

from become clogged with Bio Mix material. In this photo the excavator is covering a spur pipe with 

drainage aggregate. 44

Figure 26: Non-woven geotextile being placed on top of a synthetic liner during the construction of a 

Bioreactor. 45
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1.0 Objective

A Bioreactor is a passive treatment system component (meaning no machinery or daily chemical addition 

required for its operation) that is typically used to treat acidic or alkaline mine drainage.

The objectives of this overview are to: (1) Provide a basic understanding of the theory and application of 

Bioreactors and (2) Provide an overview of the Bioreactor Module to guide users in developing an 

estimate of the cost to construct, operate, and maintain Bioreactors for treating mine drainage. Therefore, 

this overview will be presented in two sections, Treatment Component Overview and Bioreactor

Module Overview. 

2.0 Treatment Component Overview

The following section is organized into three sections, (1) Physical and Hydraulic Description and (2) 

Application and Treatment Chemistry, and (3) Bioreactor Conceptual Treatment Module. The first section

provides a physical description and hydraulic profile for a Bioreactor to provide context for users of 

AMDTreat. The second section describes the common application of the Bioreactor component, and the 

third section shows a generalized conceptual model describing the treatment chemistry to help familiarize 

users with terms and concepts presented throughout the AMDTreat modules.

2.1 Physical and Hydraulic Description

The term “Bioreactor” is a generic term used to describe a reactor that utilizes biological-mediated 

reactions for water treatment. Each industry uses the term Bioreactor to describe an archetypical treatment 

system unique to that industry. Thus, it is important to properly describe the type of treatment system 

inferred when the term Bioreactor is used to describe its’ use in coal mine drainage treatment in the 

Eastern U.S. The proceeding discussion describes the Bioreactor treatment component represented and 

modeled in AMDTreat. 

A Bioreactor is an impoundment consisting of four or five distinct “material layers” (Figures 1 and 2). 

Whereas Vertical Flow Ponds (VFP) contain a layer of compost overtop a layer of limestone, Bioreactors 

differ in that they contain a single homogenized mixture of biomass and limestone in one layer. The 

Bioreactor biomass is a mixture of limestone fines, manure, hay and wood chips with some designs 

calling for very specific species and mixture percentages (Figures 3 & 4). Limestone or other stone is 

typically used even if the water is net alkaline to help preserve porosity and maintain open flow paths. 

The size of stone varies depending on the designer’s preference, but most stone mixed into the Bio Mix 

layer is less than 3⁄4” and often it is 1⁄4” in diameter (commonly referred to as fines). Without such a 

matrix, decaying biomass would eventually compact and cause hydraulic failure. Both wood chips and 

stone help to provide some level of porous structure to the manure and hay. 

The Bio Mix layer is typically 3.0 to 4.0 ft deep and a 2.0 to 4.0 ft freeboard layer is used to allow head 

pressure to build up and help force water through the Bio Mix layer as permeability decreases due to 

material decay and compaction. In the field, a Bioreactor looks identical to a VFP since both have a 

water layer that covers the reactive materials, and both have a similar piping design. Water flows into the 

Bioreactor at the top of the freeboard layer and flows vertically through the water layer and then through 

the Bio Mix layer. Water is collected through a collection piping network at the bottom of the 
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impoundment typically contained within a drainage aggregate layer and transported through the 

embankment to a conveyance ditch and/or oxidation/settling pond. The collection piping network (i.e. 

trunk & spur pipes) is bedded in aggregate to protect the perforated pipe from becoming clogged by

organic debris from the Bio Mix layer (Figures 5 through 9).

Many Bioreactors have flush values installed on the effluent pipe; however, they are rarely flushed to 

avoid compacting the Bio Mix layer by inducing a sudden drop in pore pressure and the fear of clogging 

the perforated pipe with the Bio Mix layer materials. In addition, long duration flushing is not advised as 

anoxic conditions must be maintained within the Bio Mix layer to prevent metal sulfide oxidization. 

However, periodic short duration flushes can occur to keep the effluent pipes clear of iron sulfide, 

elemental sulfur, calcite, microbial mats, and other debris that can accumulate within the collection piping 

network and effluent pipe. Figure 10 shows a picture of a short-term flush of elemental sulfur from a 

Bioreactor effluent pipe. 

Proper planning is required for mixing and placing the Bio Mix layer materials. It is important to create a 

homogenized mixture to prevent variations in permeability that will result in short circuiting of flow. It is 

important to discuss with the contractor the different ways to uniformly mix the different Bio Mix 

components to ensure a homogenized mixture. Additionally, the Bio Mix layer must be carefully placed 

to avoid compaction (Figures 11 through 13). There have been instances of newly constructed 

Bioreactors not being able to transmit the flow through the system due to compaction issues caused by 

improper construction techniques associated with the placement of the Bio Mix layer. Finally, estimating 

the amount of Bio Mix layer materials required can be difficult due to the decrease in volume that occurs 

when the organic materials are saturated and slightly compacted. Users can adjust the “shrinkage factor” 

variable in AMDTreat to increase the volume of dry materials to account for the shrinkage that will occur 

when the materials are mixed and saturated. Often, newly constructed Bioreactors are initially filled and 

then allowed to sit and incubate to promote microbial growth and create a low redox potential to prepare 

the Bioreactor for treatment (Figure 14). 

2.2 Application and Treatment Chemistry

A Bioreactor is a type of “passive” treatment system component used to treat net-acidic or net-alkaline 

mine drainage. The term “passive” refers to the inability to exert operational control to adjust treatment 

in response to changing influent or effluent conditions. Net-acidic mine drainage describes solutions that 

contain more acid-producing than acid-consuming species when the water is “treated”, and net alkaline 

mine drainage contains an excess of acid-consuming species. 

The primary objective of Bioreactors is to precipitate pollutants (dissolved metals) as sulfide minerals. 

Whether an additional objective of a Bioreactor is to generate alkalinity depends on whether the 

Bioreactor is treating net acidic or net alkaline water. The decision to precipitate a dissolved metal 

pollutant as a sulfide mineral, as opposed to hydroxide, is largely based on sulfides having a lower 

solubility, thus lower dissolved metal effluent concentrations can be achieved. Figure 15 shows the 

difference between sulfide versus hydroxide solubility for selected elements. For example, the lowest 

solubility for Zn(OH)2 is ~ 3.0 mg/L at pH 10, however, a concentration of 0.0003 mg/L can be achieved 

at pH 5.0 if precipitated as ZnS. Figure 16 is a phase diagram for the iron sulfur system. Bioreactors 

produce a biogeochemical environment, mostly through the use of easily oxidizable organic matter to 

create anerobic/anoxic conditions, to lower the redox potential of the system to promote chemical 

reduction and metal sulfide precipitation. Mine drainage entering the Bioreactor will typically plot within 
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the sulfate stability field and end up in the pyrite stability field after flowing into the Bio Mix layer, note 

the direction of the arrow on Figure 16. Thus, measuring and tracking both pH and Eh of a Bioreactor 

provides useful information on the condition and health of the Bio Mix layer. 

While lower concentrations can be achieved by precipitating dissolved metal pollutants as sulfides, there 

are other factors to consider when selecting the most appropriate type of passive treatment system for a 

site. Most reductive reactions are biologically mediated; thus, the kinetics are dependent on nutrients, 

temperature, pH, and other factors that are difficult to control. For example, Figure 17 shows how 

seasonal temperatures affect sulfate reduction and alkalinity production. In general, there is a large 

difference between the influent and effluent sulfate concentrations in the warmer months and smaller 

difference in the colder months. In addition, the graph shows a gradual decline in effluent alkalinity as the 

easily degradable organic matter is depleted over time. Even with a gradual decline in alkalinity over a 

five-year period, the seasonal effect on alkalinity production is still apparent. In the winter of 2008, there 

was very little sulfate reduction (influent sulfate ≈ effluent sulfate). In addition to temperature effects, the 

kinetics of sulfate reduction are pH dependent with effective sulfate reduction occurring when the pH is 

greater than 5.5. Thus, limestone is required for low pH water but may not be required for alkalinity 

production for circumneutral pH mine drainage.

For certain effluent criteria Bioreactors will be the only passive treatment option because of the low

solubility of metal sulfides, however, in most other situations other limestone-containing passive 

treatment components should be considered due to their advantages. First, unlike vertical flow ponds and 

limestone beds, metal acidity is not released and treated but rather is precipitated and stored within the 

Bioreactor. Thus, at some future time (i.e. during system rehabilitation) the acidity stored in the sulfide 

minerals within the Bio Mix layer will have to be permanently stored in a reducing environment to 

promote stability or amended with an alkali reagent and allowed to oxidize to produce a stable oxide 

mineral phase. This is a disadvantage compared to other limestone passive systems which precipitate 

stable metal oxides and hydroxides. Precipitating and storing large amounts of metal sulfide poses a 

problem and there have been instances where metal sulfides started to oxidize, and Bioreactor effluent 

sulfate concentrations are greater than the influent. In addition, Bioreactors are difficult and expensive to 

build compared to most other alkalinity producing passive components and can have permeability issues 

over time as organics within the Bio Mix layer decay. Bioreactors should not be placed near residential or 

public areas due to nuisance odors and excess hydrogen sulfide gas production in the effluent. There have 

been several instances of odor complaints made by residents living within a half mile of Bioreactors. 

Finally, precautions must be taken when Bioreactors are first saturated after construction as they will 

discharge elevated amounts of Biochemical Oxygen Demand (BOD), Chemical Oxygen Demand (COD), 

and nutrients for several months and if not adequately addressed within the system can pose a significant 

risk (i.e. reduced dissolved oxygen) to receiving streams. (Figures 18 & 19). For these reasons, 

Bioreactors should only be used in situations where no other alkalinity producing treatment components 

can achieve the applicable effluent criteria or system goals. 

2.3 Bioreactor Conceptual Treatment Model

The following discussion presents a conceptual treatment model for Bioreactors treating low pH mine 

drainage containing aluminum, iron, aluminum, and/or manganese:

2.3.1 Water Layer: It is important to maintain at least a 2 ft deep water layer to help preserve a 

reducing environment in the Bio Mix layer. The low pH discharge will first enter the water layer and 
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will have gas exchange reactions with the atmosphere (O2 in-gassing). In addition, CO2(g) will 

increase in the water layer as bubbles of CO2 gas produced from the oxidation of organic matter in the 

Bio Mix layer rise to the water layer (Figure 20). In some cases, low-pH biotic iron oxidation and 

precipitation occurs in the water layer due to the nutrients from the Bio Mix layer and the low pH

condition of the water. Often a layer of dense ferric iron precipitate will form at the interface between 

the Bio Mix and water layers that can cause permeability issues (Figure 21).

2.3.2 Bio Mix Layer: The pH will increase as mine drainage flows from the water layer into the Bio 

Mix layer. Carbonic acid and pH acidity will react with limestone fines and cause the pH to increase 

and strong aluminum precipitation will occur as the pH reaches 5.5. Dissolved oxygen will be 

consumed by the oxidation of organic matter and the redox condition of the layer will decrease. 

C6H12O6 + 6O2 = 5CO2 +H2O

Spent mushroom compost can be used in Bioreactors in the Eastern U.S. due to its availability and 

since the compost contains remnants of nutrients from fertilizer added to enhance the growth of 

mushrooms. As a result, dissimilatory nitrate reduction may occur. 

CH2O + NO3

- + 2H+ = CO2 + 1⁄2 N2 + H2O

A decreasing redox condition along with various mechanisms will cause sulfate and ferric iron to 

reduce to sulfide and ferrous iron and iron monosulfide (FeS) will form. The continued production of 

CO2 along the flow path will further drive limestone dissolution and the solution may even achieve 

equilibrium with calcite. There have been some instances of a slight decrease in manganese, 

presumably due to adsorption reactions, but most Bioreactors do not remove significant 

concentrations especially not consistent enough to be considered a form of manganese treatment. 

Alkalinity production from sulfate reduction and limestone dissolution, coupled with high 

concentrations of carbon dioxide, can achieve alkalinity concentrations ranging from several hundred 

to over one thousand mg/L as CaCO3. As the highly reduced water exits the Bioreactor, O2 ingassing can oxidize the sulfides and cause the precipitation of elemental sulfur. In addition, CO2

outgassing will raise the pH and the solution may become supersaturated with respect to calcite and 

result in calcite precipitation. Both elemental sulfur and calcite are whitish-colored precipitates. 

Figure 22 is a picture of a Bioreactor effluent where the milky-white water flowing through the rock 

energy dissipater contains both elemental sulfur and calcite precipitates. It is important to have a 

settling pond after a Bioreactor to capture these and other precipitates. In addition, it is important to 

have ample turbulence and hydraulic drops between the Bioreactor and settling pond to promote the 

oxidation of reduced sulfur species and outgassing of H2S gas before discharging the effluent to the 

receiving stream. The oxygen addition will also help to decrease the increased BOD and COD 

concentrations that typically occur in a Bioreactor effluent.

Bioreactors will have a redox boundary within the Bio Mix layer that separates oxidizing and 

reducing conditions. The boundary will migrate downwards over time as the easily-oxidizable carbon 

is exhausted and dissolved oxygen and other electron acceptors can exist and penetrate further down 

within the Bio Mix layer. As the boundary approaches the bottom of the Bio Mix layer, the 

Bioreactor can discharge ferrous sulfide and this may signify that the redox boundary is near the 

bottom and the Bio Mix layer requires replacement or there is insufficient retention time and/or 

carbon source to reduce the iron and sulfate higher up in the Bio Mix layer. Figure 22 shows a black 

precipitate of iron monosulfide at the base of a Bioreactor effluent pipe. Hydrogen peroxide was 

added to the black precipitate to oxidize the iron sulfide to ferric hydroxide in order to confirm the
9 

iron monosulfide mineral. There are several instances where the replacement of the Bio Mix layer 

was neglected, and the Bioreactor started to discharge over 60 lbs/day of suspended iron monosulfide 

to a settling pond (Figure 23). It is difficult to control the redox condition of a pond and without 

proper control tons of iron monosulfide could oxidize and discharge a large load of acidity to a 

receiving stream. For these reasons, Bioreactors need to be properly sized, have enough monitoring, 

and a safety plan to prevent oxidation and discharge of stored acidity in the form of metal sulfides. 

2.3.3 Drainage Aggregate Layer: The Drainage Aggregate Layer is discussed in more detail in the 

Layer Materials section, as it doesn’t perform a specific purpose pertaining to geochemistry treatment 

of the mine drainage. 

2.3.4 Pipe Layer: The Pipe Layer is discussed in more detail in the Layer Materials section, as it 

doesn’t perform a specific purpose pertaining to geochemistry treatment of the mine drainage.

2.3.5 Liner Layer: The Liner Layer is discussed in more detail in the Layer Materials section, as it

doesn’t perform a specific purpose pertaining to geochemistry treatment of the mine drainage.

3.0 Bioreactor Module Overview

3.1 Layout and Workflow

In general, inputs are on the left-hand side of the module and calculated outputs are on the right. The 

module inputs on the left-hand side are arranged into five sections: (1) Water Quality and Flow Input, (2) 

Sizing Methods, (3) System Properties, (4) Layer Materials, and (5) Other Items. The workflow for the 

module is for users to start at the top left-hand side. Enter the Design Flow and Net Acidity. The user then 

selects a sizing method to determine the amount of Bio Mix layer materials are necessary for the 

Bioreactor. Next, users specify design parameters such as the depth of the Bio Mix layer, and unit costs 

for items affecting the capital cost to construct the Bioreactor. Finally, users can enter any capital cost not 

captured by the module into the Other Items section. 

Module output is provided on the right-hand side of the module. Module outputs on the right-hand side 

are arranged into four sections: (1) Sizing Summary, (2) Capital Cost, (3) Annual Cost, and (4) Net 

Present Value. The sizing summary provides dimensional details for the system. The estimated cost to 

construct and operate the Bioreactor is provided under the Capital Cost and Annual Cost headings. Lastly, 

users can opt to conduct a Net Present Value (NPV) to obtain the total cost to operate and maintain a 

treatment system for a defined time period. 

A general overview of the module input and output sections is presented below, however, users are 

directed to the numerous tool tips located in the module that provide additional detailed information, such 

as definitions of terminology. In most cases, the tool tips are accessed by clicking on the information icon 

( ) in each of the subheadings in the module. 

3.2 Module Inputs

3.2.1 Water Quality and Flow Input: The Water Quality and Flow Input section is where users 

specify the design flow and water quality to size the passive treatment system component. The 
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definitions for the required input can be found in the tool tip for this section. Click on the information 

icon ( ) on the right side of the Water Quality and Flow subheading. 

3.2.2 Sizing Methods: The module offers two different approaches to sizing Bioreactors. The first 

approach calculates the volume of the Bio Mix layer before determining other dimensions. Users can 

select from four different methods to calculate the volume of the Bio Mix layer (see each method 

described below). The second approach requires users to specify the top length and width of the 

freeboard before calculating the remaining dimensions of the Bio Mix layer. The first approach is the 

most common as it relates the sizing of the treatment component based on flow and water quality 

characteristics. The second approach is common when the land area available for treatment is 

restricted or when someone wants to reverse engineer or develop a cost estimate for an existing 

treatment system component.

Volume of Bio Mix Sizing Methods (Bio Mix Layer) 

3.2.2.1 Sulfate Reduction – The user enters a rate of sulfate reduction (moles of sulfate 

reduced per volume of Bio Mix per day) along with the amount of sulfate to be reduced, 

AMDTreat uses this information along with the design flow rate to calculate a sulfate 

reduction load and a required Bio Mix layer volume. Users can specify the makeup of the Bio 

Mix layer by adjusting the material percentages and densities under the Bio Mix subheading 

located under the Layer Materials section. The “Other Percentage” and “Other Density” 

input boxes under the Bio Mix subheading can be used to specify additional materials other 

than manure, hay, limestone fines, and wood chips. AMDTreat utilizes the user-specified 

“shrinkage factor”, located under the Bio Mix subheading, to increase the volume of the Bio 

Mix layer to account for the volume reduction that occurs when the materials are saturated 

and compressed. After the volume of the Bio Mix layer is determined, AMDTreat uses the 

values for side slopes and water and freeboard depth to calculate the remaining dimensions of 

the Bioreactor. 

3.2.2.2 Alkalinity Generation Rate - This method calculates the volume of the Bio Mix layer 

required based on an expected rate of alkalinity production, or acidity neutralization, per unit 

area of Bio Mix layer. Since the depth of the Bio Mix layer in Bioreactors is commonly 3 

feet, the alkalinity generation rate could be viewed as the alkalinity production per unit 

volume (ft3

). Penn State University professor emeritus Dr. Art Rose developed this method 

(Rose, 2004) for vertical flow ponds (see VFP help file) so the default value is for sizing a 

VFP but this method may be used to size Bioreactors based on a predicted rate of alkalinity 

generation. AMDTreat calculates the volume of Bio Mix layer by dividing the daily influent 

acidity load of the mine drainage (g/day) by the user-specified alkalinity generation rate 

(g/m2

/day) to calculate the Bio Mix layer surface area requirement (m2). The surface area is 

multiplied by the user-specified Bio Mix layer depth to determine the volume required in the 

Bio Mix layer. AMDTreat utilizes the user-specified values for the different Bio Mix 

materials (specified under the Bio Mix subheading) along with the shrinkage factor to 

calculate the volume and mass of the Bio Mix layer.
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See Section 3.2.2.5 to 3.2.2.7 for volume calculations for the other layers.

3.2.2.3 Pilot Test Results - If users have their own method for determining the volume of Bio 

Mix required for the treatment of mine drainage, the Pilot Test Results sizing method should 

be used to size the Bioreactor. Often lab (bench) or pilot testing is used to help with 

Bioreactor design and these tests can reveal a volume and mixture proportions (percentage) of 

Bio Mix required to treat each gallon per minute of discharge flow. Users can specify the 

cubic feet of Bio Mix required to treat each gallon per minute of flow to determine the 

volume of the Bio Mix layer. AMDTreat utilizes the user-specified values for the different 

Bio Mix materials (specified under the Bio Mix subheading) that the user may have 

determined during testing along with the shrinkage factor to calculate the volumes and 

masses of the different materials that make up the Bio Mix layer.

3.2.2.4 User-Specified Dimensions - Mine drainage discharges often emerge at the base of 

hillsides and the available land area, between the point of emergence and the receiving 

stream, for constructing a treatment system can be limited. The use of other sizing methods 

may produce a Bioreactor that is larger than the available land area. Some folks may accept a 

smaller Bioreactor size, but this will most likely require more maintenance and prematurely 

plugging due to high metal loading per unit area/volume or only treating a portion of the mine 

drainage and bypassing the rest both resulting in limited improvements. Additionally, the 

Bioreactor may have insufficient retention time to precipitate and settle iron sulfide so the 

system could discharge iron sulfide solids, which is highly undesirable considering its 

instability and a stored source of acidity in the subsequent components of the system. In 

these cases, users can utilize this sizing method by entering the top length and width of the 

freeboard and AMDTreat will account for the user-specified side slopes and layer depths to 

calculate the dimensions and volumes of the selected Bioreactor layers.

3.2.2.5 Volumetric Calculations – AMDTreat models all passive treatment systems, including 

Bioreactors, as an “inverted” trapezoidal prism (Figure 1). AMDTreat calculates the overall 

dimensions of a passive treatment system by first breaking up the system into individual 

layers, such as the freeboard layer, water layer, bio mix layer, drainage aggregate layer, etc. 

Each individual layer and the geometric shape of the overall system is modeled as an inverted 

trapezoidal prism. AMDTreat sizing methods fall into one of two categories: (1) Users input 

information that is used to calculate a layer volume or surface area is calculated or users 

specify the mass of limestone, (2) Users specify the top width and length of the freeboard. In 

either case, AMDTreat uses the information generated by the sizing method, along with user-
12 

specified depths, side slopes, and length to width ratios to determine the dimensions of a layer 

shaped as an inverted trapezoidal prism. What differs is the approached used to calculate the 

geometry. 

3.2.2.6 Calculations for Sulfate Reduction, Alkalinity Generation Rate, and Pilot Test Sizing 

Methods – The equation for an inverted trapezoidal prism is: 

Where: 

V = Volume of trapezoidal prism

LTWT =Length & Width of top of prism

LBWB =Length & Width of bottom of prism

D = Depth

These sizing methods determine the volume of the Bio Mix layer. Therefore, AMDTreat

calculates the volume of the Bio Mix layer and users are required to specify the depth of 

the Bio Mix layer, inside slope, and length-to-width ratio for the bottom of the Bio Mix

layer. The unknowns are the length and width of the top and bottom dimensions of the 

trapezoidal prism for the Bio Mix layer. Since the depth and inside side slope of the 

Bioreactor is known, the top width and length of the Bio Mix layer can be written in 

terms of the bottom length and width to reduce unknowns in the equation. Furthermore, 

since the bottom length-to-width ratio is known, the bottom width can be written in terms 

of the bottom length. Now Equation (8) is rearranged to solve for the bottom length of 

the Bio Mix layer. The resultant equation is a quadratic: 

Where: 

V = Volume of Bio Mix Layer 

LBLL = Bottom Length of Bio Mix Layer

D = Depth of Bio Mix Layer

S = Inside Side Slope of Bioreactor 

R = Length to Width Ratio of Bottom of Bio Mix Layer
13 

Once the bottom length is known, the bottom width of the Bio Mix layer (WBWB) is 

calculated by dividing the bottom length by the user-specified value for length-to-width 

ratio for bottom of the Bioreactor: 

The two remaining unknown dimensions of the Bio Mix layer are the top length and 

width. 

The top length of the Bio Mix layer is calculated by: 

Where: 

LTLB =Top Length of Bio Mix Layer

LBLB = Bottom Length of Bio Mix Layer 

DBL = Depth of Bio Mix Layer

S =Inside Side Slope of Bioreactor (rise/run)

The top width of the Bio Mix layer is determined by the same approach. Now that all the 

dimensions of the Bio Mix layer are known, the dimensions of the water and freeboard

layers can be determined since a similar approach: 

Water Layer

The bottom length of the water layer (LBWL) is equal to the top length of the Bio Mix 

layer (LTLB). 

The top length of the water layer (LTWL) is calculated by: 

Where: 

S =Inside Side Slope of Bioreactor (rise/run)

DWL = Depth of Water Layer
14 

The same approach used to calculate the bottom and top width of the water layer. Then 

Equation (3) is used to calculate volume of the water layer.

Freeboard Layer

The bottom length of the freeboard layer (LBFL) is equal to the top length of the water 

layer (LTWL). 

The top length of the freeboard layer (LTFL) is calculated by: 

Where: 

S =Inside Side Slope of Bioreactor (rise/run)

DFL = Depth of Freeboard Layer\ 

Equation (3) is used to calculate the volume of the freeboard layer. 

In addition to assuming all passive treatment systems are constructed as an inverted 

trapezoidal prism, an additional assumption is that the excavation volume is equal to the 

summation of all the individual layer volumes, except for the freeboard layer. It is 

assumed the freeboard layer is constructed with a portion of the excavated earth. 

trapezoidal prism: Thus: 

BBBBBBBBBBBBBBBBBBBB EEEE EE EE VV oooooo

= WW VV + BBBBBB MM VV + DD DD AA (1111)

3.2.2.7 Calculations for User-Specified Dimensions Sizing Method – When users specify the 

top width and length of the freeboard for a system, AMDTreat uses the user-specified values 

for inside side slope and the freeboard, water, and bio mix layer depths to calculate the 

dimensions and volumes of the individual layers of the Bioreactor. 

The bottom length of the freeboard layer (LBFL) is calculated by: 

Where: 

LBFL = Bottom Length of Freeboard Layer 

LTFL =User-Specified Top Length of Freeboard Layer

DFL = Depth of Freeboard Layer

S =Inside Slope of Bioreactor (Run/Rise)
15 

The bottom width of the freeboard layer is calculated using the same approach. 

The volume of the freeboard layer is determined by: 

Where: 

VFL = Volume of trapezoidal prism-shaped Freeboard Layer

WTFL = Top Width Freeboard Layer

LTFL = Top Length Freeboard Layer 

WBFL = Bottom Width Freeboard Layer 

LBFL = Bottom Length Freeboard Layer 

DFL = Depth of Freeboard Layer

Water Layer

The top length of the water layer (LTWL) is equal to the bottom length of the freeboard 

layer (LBFL). 

Now that the top width and length of the water layer is known, the user-specified values 

for inside slope and depth of water layer are used in Equation (12) to calculate the bottom 

width and length of the water layer. Equation (13) is used to calculate the volume of the 

water layer. 

Bio Mix and Drainage Aggregate Layers 

The same approached used to calculate the dimensions of the water layer are used to 

calculate the bio mix and drainage aggregate layer. 

Lastly, the excavation volume is determined by adding the volumes for the water, bio 

mix, and drainage aggregate layers (Equation 16). The model assumes the excavated 

earth is used to construct the freeboard layer and any excess material is disposed of onsite. 

3.2.3 System Properties: The Systems Properties section allows the user to input the inside slope of 

the pond, the limestone layer bottom length-to-width ratio, and the excavation unit cost. AMDTreat 

suggests default quantities and unit costs for construction of a single Bioreactor.

3.2.4 Layer Materials: Unlike active treatment systems, which require the continuous addition of 

chemicals to maintain treatment of mine drainage, passive treatment systems typically consist of 

impoundments filled with enough reagent (e.g., Bio Mix) to provide treatment for many years. For 

some passive treatment system components, such as vertical flow ponds (VFP), different reagents are 

used at different elevations within the impoundment to manipulate the geochemistry and control 
16

oxidation/reduction and solubility reactions as the mine drainage flows through the component. 

AMDTreat considers each reagent or material as a “layer” in the impoundment. Both “reagent” and 

“material” are used to describe layers because not all layers are comprised of reagents or materials 

meant to manipulate water chemistry. For example, the freeboard layer is designed to accommodate 

fluctuations in flow or increasing water elevation due to permeability or plugging of layer materials 

from metal hydroxides or sediment. The piping layer is located at the very bottom of the 

impoundment and is designed to transport water out of the system or flush the system in order to 

remove metal hydroxide precipitates that accumulate in the Bio Mix or limestone layer. The Layer 

Materials section is where users can control the depth and other characteristics of the materials/layers 

used in a Bioreactor or whether to even include a layer based on a designer’s preferences. 

3.2.4.1 Freeboard Layer: Users specify the depth of the freeboard layer designed to produce 

enough storage to accommodate increases in the water layer due to increased flow events or 

clogging of the treatment media in lower layers. Since the Bio Mix layer has lower initial 

permeability than limestone-based systems and loses permeability as the organic matter decays 

and compacts, Bioreactors may have more freeboard than other types of passive components. 

Designers may want to consider having a foot of freeboard for every foot of Bio Mix layer to 

ensure hydraulic head can increase to force flow through the Bio Mix layer as permeability 

decreases. As with most passive components, the influent to the Bioreactor is within or at the top 

of the freeboard layer. An emergency spillway is incorporated into the freeboard layer just below 

the influent elevation (if the top of the water layer is lower than the influent elevation) to prevent 

the restriction of water flowing into the Bioreactor and to prevent water from overtopping the 

embankment. The bottom of the freeboard layer is the top of the water layer for the Bioreactor. A 

typical freeboard layer depth for a Bioreactor is 2.0-3.0 feet.

3.2.4.2 Water Layer: The water layer maintains the saturation of the treatment media and helps to 

disperse the water flow across the surface area of the Bioreactor. The depth of the water layer is 

often manipulated to maintain equilibrium as the treatment media clogs with sediment or metal 

hydroxide precipitates and to control gas exchange of the lower layers with the atmosphere. At 

times, the water elevation may need manipulated to control the growth of aquatic plants that may 

occur in Bioreactors. A typical water layer depth is between 2.0 and 3.0 feet. Bioreactors may 

have deeper water layer depths to help maintain anoxic conditions in the Bio Mix layer. 

3.2.4.3 Bio Mix Layer: The Bio Mix layer typically consists of manure, hay, limestone fines, and 

wood chips to create an anerobic environment for sulfate reduction to occur. The purpose of the 

Bio Mix layer is to create a geochemical environment to induce sulfate reduction and metal 

sulfide precipitation. In addition, the Bio Mix layer is the source of alkalinity generation in a 

Bioreactor. Users can specify the layer depth, shrinkage factor, percent composition, density, and 

unit cost for each material to be used and the mixing/placement of the Bio Mix layer in this 

section. The Bio Mix depth is typically 3.0 to 4.0 feet and must contain a supportive matrix, 

such as stone and/or wood chips, to maintain permeability as the manure and hay decay.

3.2.4.5 Drainage Aggregate Layer: For Bioreactors, it is very important to embed the effluent 

piping network in an aggregate layer to protect the perforated pipes from becoming clogged with 

the Bio Mix layer materials (Figures 6, 7 & 24). The drainage aggregate layer is used to calculate 

the amount of aggregate required to embed the effluent pipe network. Note, the drainage 
17

aggregate layer depth should be equal to or greater than the largest diameter pipe to be used in the 

collection piping network (trunk and spur pipes).

3.2.4.6 Pipe Layer: The piping layer considers the piping required to convey the water into and/or 

out of the Bioreactor. The majority of the piping layer is situated between the Bio Mix and liner 

layers. Additionally, the piping layer in AMDTreat accounts for the influent/effluent pipes. The 

Bioreactor module offers users two methods to estimate the cost to purchase and install a piping 

network, the AMDTreat Piping Calculator or User-Specified Piping Layout. The default design of 

the AMDTreat Piping Calculator for a Bioreactor is the same as for a Vertical Flow Pond (VFP). 

The effluent piping network consists of a “trunk” pipe that extends the bottom length of the 

Bioreactor and “spur” pipes that extend the width of the system and are connected perpendicular 

to the trunk pipe. Users can specify the distance between the spur pipes by manipulating the Spur 

Pipe Spacing values in the Pipe Layer subheading. The spur pipes are attached to the trunk pipe 

using a “tee” connector while the trunk pipe may be connected to the effluent pipe using a 

coupler depending upon the pipe orientation.

3.2.4.7 Liner Layer: Many mine sites lack the soil characteristics required to prevent leaky 

passive treatment system components. AMDTreat offers three types of liner systems that prevent 

water leakage from the impoundment(s), including Clay, Synthetic (i.e. PVC), and Geosynthetic 

Clay (GCL) liners. The volume of clay liner required is calculated from the entire inside sloped 

area of the pond, from the top of freeboard to the base of the drainage aggregate layer (bottom of 

pond), plus the bottom area of the Bioreactor and multiplying it by the user-specified compacted 

thickness (typically 0.5 to 1.0 foot) and unit cost to purchase and install the clay liner. The area 

required for synthetic or GCL liners is determined by calculating the inside sloped area and the 

bottom area of the Bioreactor similar to the clay liner and adding an additional 2.0 ft of length on 

all sides to accommodate the incorporation (“tie in”) of the liner into the embankment near the 

top of the freeboard layer to secure the liner system. AMDTreat provides the option of adding 

non-woven geotextile as a separate material for all liner systems. Non-woven geotextile 

separation material is commonly used to protect the synthetic or geosynthetic clay liner from the 

excavated inside surface of the pond and/or the limestone layer from the excavated surface of the 

pond or selected liner material. Figure 25 shows non-woven geotextile being placed on top of a 

synthetic liner during the construction of a Bioreactor.

3.2.5 Other Items: The Other Items section allows users to consider the capital cost of inlet and outlet 

structures, valves, and flow distribution structures. AMDTreat suggests default quantities and unit 

costs for construction of a single Bioreactor. 

3.3 Module Outputs

3.3.1 Sizing Summary: The Sizing Summary section contains all the calculated module outputs, such as 

the dimensions, volumes, and plug flow retention times for the various layers. The total mass of Bio Mix 

materials required for the Bio Mix layer is provided on the right-hand side of the Sizing Summary 

heading, which is further broken down by material within this section.
18 

3.3.2 Capital Cost: This section provides the estimated costs for the various user-specified components 

and the total estimated cost to construct the entire Bioreactor component of the passive treatment system.

3.3.3 Annual Cost: Since a Bioreactor is a passive treatment system component, the only annual cost 

considered is the cost for maintenance. Annual costs, such as sampling, labor, and access road 

maintenance are “project-wide” costs since they apply to an entire treatment site, not each individual 

treatment component. Sampling, Labor, and Site Development (i.e. snow plowing) modules are located 

under the “Project Modules” section of the Main User Interface and capture these types of annual costs. 

Annual maintenance costs for Bioreactors may include periodic “flushing” of the drainage aggregate and 

piping layer to evacuate accumulated metal sulfide precipitates from the stone void spaces, maintaining 

clear influent and effluent piping, and manipulating the water level control structure (e.g. Agri drain) to 

change the water level in the Bioreactor as needed. It is assumed that some years will not require the full 

amount of funds set aside for annual maintenance but will eventually be used over the system life. Users 

can estimate the annual maintenance costs by assuming a percentage of the capital cost (more expensive 

the system, the more expensive the maintenance) or specify a known annual maintenance cost amount. 

3.3.4 Net Present Value: The Net Present Value (NPV) section determines the cost to operate a 

treatment system component over a specified time period. The NPV calculates the present-day financial 

investment required to generate the income to pay for future operation and equipment/materials

replacement costs. Both Financial Variables and Cost Categories are required to calculate the NPV. 

3.3.4.1 Financial Variables - The Term of Analysis, Inflation Rate, and Rate of Return are 

three variables used in the NPV calculations. The default values for these terms are 

shown under the Net Present Value section of each module. Users must access the Net 

Present Value menu at the top of the main user interface to change the default values as 

they would apply to all modules used for an entire treatment system. While NPV is 

determined for each AMDTreat module activated by the user, the goal is to determine a 

total NPV for an entire mine drainage treatment system project (a collection of cost 

estimates for individual modules creates a treatment system project in AMDTreat). 

Therefore, a single value for Term of Analysis, Rate of Return, and Inflation Rate is 

applied to all modules and cannot vary between modules. 

• Term of Analysis: The time period used by the NPV calculation to determine the 

financial investment required to pay for all future costs of the treatment system. 

• Inflation Rate: Represents the average price increase of goods and services over 

time. AMDTreat uses the inflation rate to calculate the future cost of the annual 

operation and maintenance (O&M) and recapitalization items. 

• Rate of Return: Describes the expected profit on an investment. 

3.3.4.2 Cost Categories - For each treatment module, AMDTreat provides a list of 

recommended equipment and materials that require recapitalization. In addition, 

AMDTreat provides recommendations (default values) for life cycle and replacement 

percentage. Users can click on the default values for Life Cycle or Replacement 

Percentage and use the +/- buttons to change the default values. In addition, users can 

select Custom Cost and enter a new cost to represent the current cost of the equipment. 
19 

Users can add new recapitalization items or deactivate/delete existing items for 

calculating the NPV. 

An example of how the recapitalization variables are used to determine NPV is to 

consider the following hypothetical scenario. Assume a vertical turbine pump has a life

cycle of 50 years but requires the pump motor to be rebuilt every 20 years. Assume the 

present-day cost to purchase the motor is $500,000, and the cost to remove, rebuild, and 

reinstall the pump motor is $20,000. Now assume we want to determine the amount of 

investment required today (NPV) to generate the income to pay for the future cost of 

rebuilding the pump motor over a 50-year Term of Analysis, which is also equal to the 

life cycle of the pump. Assume an Inflation Rate of 5.0% and Rate of Return of 8.1%. 

The goal is to place the money in a relatively secure investment vehicle to generate 8.1% 

annually. The NPV will calculate the size of investment required to generate income for 

future costs. 

There are several ways to model the replacement cost. One way is to replace 4% of the 

present-day cost of the pump (4% of $500,000 = $20,000) with a life cycle of every 20 

years. If the Term of Analysis is 50 years, then the entire pump would not require 

recapitalization since the life cycle of the pump is 50 years. However, the motor would 

require two replacements (50 years / 20 years = 2.5 rounded down to 2). 

To determine the NPV to recapitalize rebuilding of the motor, AMDTreat calculates the 

future cost to rebuild the motor at each life cycle, 20 and 40 years. The program uses the 

Inflation Rate to inflate the present-day default cost to rebuild the motor in 20 and 40 

years from now. While the present-day cost to rebuild the pump motor is $20,000, the 

future cost to rebuild the motor in 20 years at a 5.0% Inflation Rate is $53,065 and 

$140,799 in 40 years (Equation 8). Assuming an 8.1% Rate of Return, the 50-year NPV

for the pump is $17,422. In other words, an initial investment of $17,422 is needed at an 

annual Rate of Return of 8.1% to generate the investment income required for the two 

motor rebuilds over the 50-year life cycle of the pump. 

• Annual Operation and Maintenance Cost: By default, AMDTreat transcribes the annual 

O&M cost from the Annual Cost section to the Net Present Value section. The program 

assumes the module is being used to first estimate the annual cost for a treatment system 

component, so it automatically transcribes the annual cost to the NPV section. If this is 

not the case or the user wants to use some other annual cost, the “Use Custom” box can 

be selected to allow the user input of a different annual cost to utilize in the NPV 

calculation. 

• Recapitalization Cost: Certain treatment system components, especially mechanical and 

water conveyance equipment, require periodic replacement. The recapitalization cost of 

an item is an estimate of the amount of money required to pay for future replacement 

costs for the item. In addition to the Financial Variables described above, three additional 

values are required to calculate the NPV of recapitalization costs, the Present-Day 

Equipment Cost, the Life Cycle, and the Replacement Percentage. 
20 

• Default Cost: This represents the current cost to purchase the equipment or material.

• Life Cycle: The time frame between equipment or material replacement is termed as its 

Life Cycle. Some equipment manufacturers provide recommended life cycles for their 

equipment to provide consumers with an estimate of how long the equipment is expected 

to be operational. Some life cycles, such as those used for treatment media (limestone), 

are based on best professional judgement. Some operators prefer to periodically purchase 

and replace equipment before failure to preserve the continuity of operations, while 

others wait until failure to replace an item.

• Replacement Percentage: The Replacement Percentage is an adjustment factor to the 

Default Cost to accommodate situations where the entire piece of equipment or all of the 

material does not require recapitalization. For example, a passive treatment component 

may be designed to contain enough limestone to neutralize the acidity load for 20 years, 

however, the accumulation of metal hydroxide precipitates within the void space of the 

limestone layer may require that 25% of the limestone be replaced every 7 years to 

prevent hydraulic failure such as plugging or short-circuiting. For this scenario, the 

initial cost of the limestone making up the limestone layer is discounted by 75% and 

assigned a life cycle of 7 years to determine the amount of money required to cover the 

cost of replacing 25% of the limestone layer every 7 years over the Term of Analysis. 

3.3.4.3 Rationale for Recapitalization Recommendations: 

Recapitalization recommendations are based on professional experience of the 

AMDTreat Team and may not apply to all situations. Users are encouraged to customize 

the recapitalization assumptions to their treatment scenario. AMDTeat Team members 

are located in Pennsylvania and West Virginia and have collective experience in design, 

funding, and/or operation/maintenance for over 100 passive treatment systems. Most 

passive treatment systems constructed in Pennsylvania and West Virginia are less than 15 

years old, thus the industry is still gaining experience in lifecycles for various 

components. However, the AMDTreat Team held discussions on personal experience to 

develop a list of recapitalization recommendations. Users may have different experience 

and opinions. 

By default, AMDTreat includes a list of six recapitalization items for Bioreactor. The 

items are listed even if they are not selected for the treatment system. The purpose of this 

is to inform the user of items they should think about recapitalizing or including in their 

treatment design. For example, Liner is listed as a recapitalization item even if no liner is 

selected in the cost estimation. In this case the recapitalization cost is set to $0.00 but the 

item is still shown as a reminder to the user that a Liner is a common item that should be 

considered. If a liner is included in the cost estimation, the estimated liner cost is used to 

calculate a recapitalization cost for liner. Users can delete or modify any of the default 

Recapitalization items by either deselecting the item or by setting the Replacement % to 

zero. If the item is deselected the Total Cost for the item will still be shown but the cost 

will be subtracted from the Net Present Value Cost, shown in the Net Present Value 

Heading. 
21

Bio Mix: A portion of the Bio Mix may need to be replaced as it becomes less effective 

of producing anaerobic conditions. Based on the historical experience of maintain 

Bioreactors, AMDTreat recommends planning to replace 100% of the Bio Mix every 15

years.

Drainage Aggregate: A portion of the Drainage Aggregate may need replaced as it may

be become clogged with precipitate. The default assumption is to replace 50% of the 

drainage aggregate every 15 years. 

Liner: Often liners are destroyed, especially synthetic, while conducting maintenance on 

passive treatment systems, if the equipment operator is inexperienced with passive 

systems. Thus, AMDTreat recommends planning to replace a portion of the liner while 

the Bio Mix and/or Drainage Aggregate is being replaced. The default assumption is to 

replace 50% of the Bio Mix every 15 years, so the same assumptions are recommended 

for Liner recapitalization.

Pipe: Piping is often exposed at the surface and can become damaged by vandalism, 

falling trees, and other factors. AMDTreat assumes 50% of the piping will require 

replacement after 15 years of service.

Other Items: The Other Items section in AMDTreat includes Flow Distribution 

Structures, Water Level Control Structures, and Outlet Protection Structures. These 

structures are often durable, and many treatment systems have never experienced 

replacement of these items, however, AMDTreat Team members have had at least one 

experience of each of these items requiring replacement, thus the Team wanted to include 

these items for replacement consideration. 

3.4 Assumptions of Design Sizing and Costs

AMDTreat is a cost estimation model that uses assumptions to provide treatment sizing and both capital 

and annual cost estimates. While there are many assumptions in the program, the ones provided below are 

important to consider for the Bioreactor module. 

1. The Bioreactor is assumed to be constructed on a flat surface, where the water and Bio Mix 

layers are excavated or below the existing or original ground, and a portion of that material is 

used to construct the freeboard embankments which is considered fill material above the existing 

or original ground (see Figure 1). The program assumes an on-site balance of cut / fill, however, 

if this is not the case, the user can modify excavation cost default values to reflect the anticipated 

conditions based on the site characteristics. 

2. The geometric shape of a Bioreactor is an inverted trapezoidal prism. The volumetric equation 

for a trapezoidal prism is used to calculate the Bioreactor layer volumes. 

3. None of the sizing methods provide a “design life” that properly accounts for the hydraulic and 

treatment issues caused by the compaction due to the decay of organic matter and the 

accumulation of metal sulfide precipitates within the void spaces of the treatment media. 

4. In general, the goal of the Bioreactor sizing methods is to provide an estimate of the Bio Mix 

layer mass required to create a reducing environment to precipitate metal sulfides. None of the 
22

sizing methods are based on achieving effluent water quality criteria or requirements. With that 

said, a properly sized Bioreactor treatment component should generate pH > 6.0 and net alkaline 

water, which in theory will decrease aluminum and iron solubility to less than 1.0 mg/L. 

4.0 References

Hedin, R.S. and Watzlaf, G.R., 1994. The effects of anoxic limestone drains on mine water chemistry. 

Proceedings of the 3rd International Conference of the Abatement of Acidic Drainage, Volume 1, 

Pittsburgh, PA. U.S. Bureau of Mines SP 06B-94, p. 185–194.

Rose, A. W., 2004. Vertical flow systems – Effects of time and acidity relations. Proceedings, American 

Society of Mining and Reclamation, Morgantown, WV, April 18-24, 2004, p. 1595-1615. 

https://www.asrs.us/Portals/0/Documents/Conference-Proceedings/2004/1595-Rose.pdf
23

5.0 Figures 

Figure 1: Typical Inverted Trapezoidal Prism

Figure 2: Typical Cross Section View of a Bioreactor showing the 

Common Layers and Components
24

Figure 3: Plan View of the Bioreactor to Illustrate Common Piping 

Layout and Components (Used in AMDTreat Piping Calculator) and the 

Layer Surface Areas.
25

Figure 4: Staging area for making the Bio Mix. Picture shows piles of 

manure, limestone fines, wood chips, and hay bales.

Figure 5: Large pile of Bio Mix (manure, compost, hay, woodchips, 

limestone) in preparation to be placed in Bioreactor.
26

Figure 6: Lateral piping network placed overtop of non-woven geotextile 

and synthetic liner. Note the pipes placed in rock bedding to protect 

perforated openings.

Figure 7: Close up image of effluent collection pipe embedded in rock 

shown in Figure 5. Image shows spur pipes (bottom left) connecting 

into the trunk (header) pipe (bottom right).
27 

 

Figure 8. Excavator installing rock bedding for piping network.
28

Figure 9: Bioreactor under construction showing effluent collection pipe 

embedded in rock (bottom right) to be covered by Bio Mix layer. Pipe 

cleanouts were installed along the side slopes to remove debris if 

collection piping becomes clogged. Once a common practice, cleanout 

pipes are now sparingly used because of short circuiting issues 

experienced by flow along the sides of the clean out pipes.
29

Figure 10: Alternative piping network design. Spur pipes are aligned 

parallel to the longest dimension of the Bioreactor and the trunk (header) 

pipe is positioned across the width of the bioreactor. The piping network 

is embedded in stone to protect the perforations from the overlain Bio 

Mix layer.
30

Figure 11: Short term flush of a Bioreactor effluent pipe to prevent build 

up of precipitates. Whitish elemental sulfur flushed into a subsequent 

pond filled with ferrous monosulfide. FeS particulates constantly 

discharge from this bioreactor to the settling pond due to an 

insufficiently sized Bio Mix layer.
31

Figure 12: Truck end-dumping the Bio Mix material and excavator 

trying to carefully smooth out the surface to obtain a uniform thickness 

to promote a uniform flow pattern. Extreme caution must be used to 

prevent compaction of the Bio Mix material, which is irreversible.
32

Figure 13: Bio Mix being spread over top of a non-woven geotextile and 

synthetic liner system during the construction of a 2.0 acre Bioreactor.
33

Figure 14: Bioreactor filled with Bio Mix layer right before the initial 

filling with water and incubation period. Care was taken to create a 

uniform Bio Mix layer depth, however, the picture shows peaks and 

valleys within the Bio Mix that differ by up to a foot and will affect the 

flow pattern. Thus, this Bioreactor contains three separate piping 

systems (right side, middle, and left side of Bioreactor) that are 

controlled by three separate water control structures (e.g. Agri-drain 

boxes) to help equalize the uneven flow patterns caused by the variable 

thickness and homogeneity created during the construction. 
34

Figure 15: Solubility of metal hydroxide vs. sulfides for various 

elements
35

Figure 16: Pourbaix diagram for an aqueous iron/sulfur system. Most 

mine drainage would plot within the SO4

2- stability field. The goal of a 

Bioreactor is to create an Eh/pH condition that plots in the pyrite 

stability field. 
36

Figure 17: Monthly Influent and effluent sulfate concentration and 

effluent alkalinity concentrations for a Bioreactor over a five-year 

period. 
37

Figure 18: Newly constructed Bioreactor being filled with mine drainage 

in preparation for a two-week incubation period.
38

Figure 19: First discharge of a newly constructed Bioreactor after the 

incubation period. The organic-rich water with elevated BOD & COD is 

an environmental concern if not appropriately treated in the subsequent 

ponds.
39

Figure 20: Discharge of a Bioreactor into the receiving stream right after 

the incubation period. Designers did not take proper precautions to treat 

the high BOD Bioreactor effluent water during the first few months of 

operation. 
40

Figure 21: Photo showing a 3.0 by 3.0 ft area of the top of a Bio Mix 

layer under the water layer. One to two-inch diameter holes can be 

observed made by CO2 produced in the Bio Mix layer. The pH 2.7 mine 

water entering the Bioreactor and low pH iron oxidization is causing a 

ferric hydroxy sulfate mineral crust on top of the Bio Mix layer.
41

Figure 22: The milky-white water flowing out of a Bioreactor and 

through an outlet protection structure contains both elemental sulfur and 

calcite.
42

Figure 23: Black precipitate at the base of a bioreactor effluent pipe 

(black coated rocks to left of white pipe). Hydrogen peroxide is added to 

the black precipitate and the oxidation to produce an orange-red color 

ferric hydroxide confirms the precipitate as iron sulfide.
43

Figure 24: This photo is of the outfall from a Bioreactor effluent pipe. 

Note the black-colored pond in the background receiving this effluent. 

This Bioreactor contains an insufficient volume of Bio Mix layer needed 

to precipitate and settle the entire ferrous iron concentration and as a 

result ferrous sulfide (FeS) reactions continue to occur as the water is 

discharged from the Bioreactor. The Bioreactor discharges sixty (60) 

pounds of FeS as particulate matter every day, which is captured by the 

settling pond creating a potential environmental hazard in the form of 

stored acidity. To compound the seriousness of the iron sulfide 

accumulation, a drinking water reservoir is shown at the very top of the 

photo that receives the final effluent from this Bioreactor treatment 

system. 
44

Figure 25: While the photo is not a Bioreactor, the collection piping 

network shown here is the same configuration as the default piping in 

AMDTreat (if the AMDTreat Piping Calculator is used). A large trunk 

pipe extends along the center of the bottom length of the treatment 

component and spur pipes extend the width to collect and transport 

treated water out of the pond. The entire effluent piping network in a 

Bioreactor should be embedded in a drainage aggregate layer to protect 

the spur pipe perforations from become clogged with Bio Mix material. 

In this photo the excavator is covering a spur pipe with drainage 

aggregate.
45

Figure 26: Non-woven geotextile being placed on top of a synthetic liner 

during the construction of a Bioreactor.