1

Table 7-1. Summary of Qualitative Uncertainty Analysis of Key Elements Affecting the AAPI form of the NOx/SOx Standards. 

Source Description

Potential influence of 

uncertainty in element

KnowledgeBase 

uncertainty Comments 

Direction

(negative 

implies less 

relative 

protection) Magnitude

Major elements (and sub-models) of the ecological effects to ambient concentration framework

Biological/ecosystem 

response to 

acidification

Clear associations between 

aquatic acidification (pH, 

elevated Al) and adverse 

ecosystem effects (fish 

mortality, decreased species 

diversity)

Both Low Low (regionally)

The ecosystem level responses are well studied at regional 

levels. The uncertainty increases at larger scales due to an 

increasing number of factors influencing the patterns (e.g. 

latitudinal species gradient, specie-area relationships, etc.).

Linkage between 

direct acidification 

species and

ecological indicator 

(ANC)

The relationships across 

ANC, pH and dissolved Al 

are controlled by well 

defined aquatic equilibrium 

chemistry

Both Low Low

ANC is the preferred ecosystem indicator as it has a direct 

relationship with pH and the deposition species relevant to the 

NOx/SOx standard. 

Linkage between 

ecological indictor 

and adverse 

ecological effects

Direct nonlinear associations 

between ANC and fish 

mortality and species 

diversity

Both Lowmedium Low

Although the pH dependency on ANC is nonlinear, it is always 

directionally consistent. In extremely low and high ANC 

environments the relationship is of minimal value as 

catchments are in relatively “less sensitive” regimes due to 

natural conditions or extreme anthropogenic influence (i.e., 

acid mine drainage). In sensitive areas of concern the 

relationship essentially is similar to the relationships between 

direct acidification species and adverse effects. 

Deposition to ANC 

linkage through 

Critical Load 

approach

Mass-balance Steady State 

critical load model is applied 

to determine critical load 

values. MAGIC model is 

used to validate steady State 

model. The Steady State 

critical load model 

formulation is used as the 

foundation for deriving the 

AAPI equation.

Both Low Low

The model formulation is well conceived and based on a 

substantial amount of research and applications available in 

the peer reviewed literature. There is greater uncertainty 

associated with the availability of data to support certain 

model components.
2

Source Description

Potential influence of 

uncertainty in element

KnowledgeBase 

uncertainty Comments 

Direction

(negative 

implies less 

relative 

protection) Magnitude

Atmospheric 

concentrations to 

deposition

Deposition is a direct function 

of ambient concentration, 

influenced by several 

processes, and handled in the

AAPI through air quality 

modeling.

Both Low Low

The model design is appropriate given the spatial and temporal 

complexities that influence deposition velocity, as well as the 

variety of atmospheric species that generally are not measured. 

Greater uncertainty resides in the information (e,g,, ammonia 

emissions) driving these calculations and availability of 

observations to evaluate model behavior.

Ecological indicator 

to changes in the 

value of ecosystem

services

Definitions of public welfare

may include economic 

considerations, based on the 

tradeoffs people would make 

to avoid the negative impacts 

of acidification, through 

effects on the values of 

ecosystem services. 

Empirical estimates of 

valuation for limited 

ecosystem service categories 

are used to inform the 

discussions of adversity 

associated with alternative 

ANC levels.

Negative Mediumhigh Low-medium

There are many studies that estimate the value of increasing 

services that may be affected by changes in acidification and 

eutrophication. However, few of these studies focus on the 

particular impact of acidification and eutrophication on the 

quality of these services and preferences for avoiding these 

impacts. 

Those studies that do are often limited to analyzing the 

impacts on a narrow population or particular change in 

environmental quality. The monetized benefits to fishers and 

to New York residents for ecosystem improvements in the 

Adirondacks associated with improvements to the ecological 

indicator are significant underestimates of the total benefits in 

the U.S. This is because those living outside New York would 

value improvements to the Adirondacks and similar natural 

environments elsewhere. 

The methodologies used in the studies that underlie the 

estimates of the value of changes in ecosystem services in the 

Adirondacks region are sound and have been subject to peer 

review. The method of aligning the improvements valued in 

the Banzhaf et al. study with estimates of eliminating current 

damages leads to may lead to an over or underestimate of the 

benefits. The range of this difference is difficult to know a 

priori, but the total improvements in the share of lakes that 

improve above an ANC threshold of 20 μeq/L are consistent.
3

Source Description

Potential influence of 

uncertainty in element

KnowledgeBase 

uncertainty Comments 

Direction

(negative 

implies less 

relative 

protection) Magnitude

Sub-components and data of individual models 

Atmospheric Components

DepSOx

Annual deposition of sulfur 

mass from dry deposition of 

(SO2 and SO4) and wet SO4

derived from CMAQ 12km 

horizontal grid resolution 

averaged over 5 years 

both low low

The treatment of SOx deposition in EPA air quality models 

has evolved over the last two decades. There is general 

consensus that the overall mass balance of S is treated well 

with difficulties in spatial pairing of observations and modeled 

results of wet deposition. This spatial pairing has improved 

with the more recent PRISM adjustments. 

DepNOy

Annual deposition of oxidized 

nitrogen mass from dry 

deposition of (all NOy 

species) and wet NO3 derived 

from CMAQ 12 km 

horizontal grid resolution 

averaged over 5 years

both low low-medium

The treatment of oxidized nitrogen deposition in EPA air 

quality models has evolved over the last two decades. There 

is general consensus that the overall mass balance of oxidized 

N is treated well. However, the broad range of deposition 

velocities across NOy species, and especially uncertainties 

regarding the deposition of significant species such as NO2

pose ongoing challenges. Similarly, a shortage of NOy 

species measurements as well a lack of techniques to directly 

measure dry deposition impede progress on improving 

parameterization of N dry deposition.

DepNHx

Annual deposition of reduced 

nitrogen mass from dry 

deposition of (NH3 and SO4) 

and wet NH4 derived from 

CMAQ 12km horizontal grid 

resolution averaged over 5 

years

both low medium

NHx deposition also is quantified through CMAQ 

applications. The well dispersed nature of agricultural based 

emissions that are influenced strongly by meteorological and 

surface /soil characteristics continues to challenge 

characterization of ammonia emissions. Recent 

incorporation of a bi-directional flux process in CMAQ 

improves consistency with available scientific understanding 

and yields improved time and space pairing of limited 

observations with model results. A lack of both ammonia and 

ammonium ambient observations continues to compromise our 

ability to characterize uncertainty in our treatment of NHx. 

As with all dry deposition estimates, technologies for direct 

measurements are not available routinely. Both NHx 

deposition and NOx deposition are assigned low values of 

magnitude based on a general dominating role of sulfur 
4

Source Description

Potential influence of 

uncertainty in element

KnowledgeBase 

uncertainty Comments 

Direction

(negative 

implies less 

relative 

protection) Magnitude

deposition. 

Wet deposition 

(generically – N and 

S species)

Wet component of total 

deposition as described in the 

Dep terms, above

both low low

Wet deposition remains an attribute of relatively high 

confidence based on the ability to directly measure chemical 

components in precipitation samples. However, given the 

stochastic nature of precipitation, models have a difficult time 

in matching observations. The use of 5 year averages and 

post-processing PRISM adjustments have reduced uncertainty 

in spatial pairing of observations and modeled estimates.

Dry deposition 

(generically – N and 

S species)

Dry component of total 

deposition as described in the 

Dep terms, above

both medium Medium-high

The absence of direct dry deposition measurements combined 

with the significant variability in the parameters that influence 

dry deposition velocity reduces the confidence level in dry 

deposition relative to wet deposition.

Deposition 

Transference Ratios

CMAQ derived ratio of total 

oxidized deposition to 

concentration averaged over 

one year

both low unknown

Transference ratios enable the connection between deposition 

and the policy relevant ambient air indicators, NOy and (SO2 + 

SO4). They are strictly a model construct and cannot be 

evaluated in a traditional model to observation context. The 

low sensitivity of these ratios to emission changes and inter 

annual meteorology combined with low spatial variability 

indicate that these ratios are necessarily stable.

CNOy

Ambient concentrations of 

NOy through observations. negative low Low-medium

Adequate spatial coverage of NOy observations does not exist, 

but will be addressed in the proposed rule. The monitoring 

technology only over the last 5 years has been perceived as 

“routine” based on incorporation in the NCore network. 

However FRM status for NOy instruments currently is not 

available. The negative bias direction is a standard caveat to 

any instrument relying on internal air stream conversion of 

atmospheric species prior to detection.

CSOx

Ambient concentrations of 

NOy through observations. both low Low

A lack of adequate spatial coverage is the primary concern for 

SO2 + SO4 observations. FRM status is not available for 

SO4; although the long track record of accurate and precise 

CASTNET FP measurements indicates that achieving FRM 

status is a low hurdle. 

Ecosystem Components
5

Source Description

Potential influence of 

uncertainty in element

KnowledgeBase 

uncertainty Comments 

Direction

(negative 

implies less 

relative 

protection) Magnitude

BC0

* Pre-industrial base cation 

concentrations negative Mediumhigh high

Both the F-factor approach and process based MAGIC 

modeling were used to generate BC0

*

. Excellent agreement

between both approaches was established in the Shenandoah 

streams. The more comprehensive data requirements of 

MAGIC limit its widespread use to the Adirondacks, although 

for consistency the F-factor approach was applied nationwide. 

The analyses also illustrated greater divergence at higher 

critical loads, or areas with greater acid buffering capacity and 

high bas cation levels. These conditions often are screened 

out of our population distribution analyses, and when included 

do not affect the location within the distribution of the more 

sensitive water bodies. Since MAGIC (the preferred 

approach) tends to overestimate BC0

*

relative to the F factor 

approach, and the F-factor is more widely applied nationally, 

the BC0

* estimates are viewed as conservative leading to a 

slight positive bias in estimating critical loads. Although we 

have many modeled estimates of BC0

*

, there is a lack of direct 

measurements of BC weathering rates.

Neco positive low medium

The term Neco, as defined, has a relatively medium confidence 

level and is a direct function of the uncertainty inherent in the 

deposition estimates from CMAQ and surface measurements 

of NO3. However, this “measurement” difference approach 

reflects the average of all influencing processes 

(dinitrification, uptake, immobilization) over the time period 

of measurements. Consequently, there is an inherent 

assumption of a relatively static system (Neco is applied in a 

steady state model) that generally is not tested. In concept, a 

true steady state vision of Neco would be based on a mature 

forested ecosystem. The relative bias of Neco is related, 

largely, to the relative productivity of the forest. The 

challenge in determining any potential bias in Neco is to 

determine the relative “maturation age” of an ecosystem which 

requires knowledge of future land use activities. In areas of 
6

Source Description

Potential influence of 

uncertainty in element

KnowledgeBase 

uncertainty Comments 

Direction

(negative 

implies less 

relative 

protection) Magnitude

high land use restrictions of a recovering forest, Neco would 

be assumed to be overestimated. The relative magnitude of 

Neco often is mitigated by the dominance of SOx in 

controlling acidification processes in many systems. 

Furthermore, it is unclear to what extent any stored N will be 

released back into the system, which is assumed to not occur 

in the linked system model. 

Q

Annual runoff rate 

(distance/time) for a 

catchement.

both low high

Data used to calculate Q was compiled in 1985. Streamflow 

data were collected at over 12,000 gauging stations during 

1951-80; 5,951 stations were selected for the analysis. See 

Gebert and others (1987) for a complete description of how the 

runoff was determined from the streamflow data. Appropriate 

maps of the data can show the geographical distribution of 

runoff in tributary streams for the years 1951-80 and can 

describe the magnitudes and variations of runoff nationwide. 

The data was prepared to reflect the runoff of tributary streams 

rather than in major rivers in order to represent more 

accurately the local or small scale variation in runoff with 

precipitation and other geographical characteristics.

t, W.A., Graczyk, D.J., and Krug, W.R., 1987, Average annual 

runoff in the United States, 1951-80: U.S. Geological Survey 

Hydrologic Investigations Atlas HA-710, scale 1:7,500,000. 

DOC Surface water dissolved 

organic carbon negative low medium

Water bodies with high DOC levels (> 10mg/l) were screened 

out of the critical load calculations in order to avoid naturally 

acidic systems. However, the inherent assumption of ANC = 

∑strong CA - ∑strong AN does not explicitly account for 

contributions of weak organic acids. Consequently, a small 

positive bias pervades the critical load calculations (i.e., the 

CL estimates are high). The knowledge base value of M 

reflects a general shortage of DOC data.