Chapter 5
Habitat Measurement

Habitat measurement is used to assess the impacts of habitat on biota, and hence on the interpretation of changes in biota. Habitat must be taken into account to make accurate comparisons between ambient and reference conditions and to determine whether habitat might be a cause of impaired biota.

Human activities modify the watershed, with consequent effects on lake physicochemical and biological processes. Agricultural and urban land use affect nutrient, contaminant, and sediment loadings; and shorezone housing development can have a disproportionate influence on nutrient loadings compared with more distant parts of a lake watershed (Dillon et al. 1994). Shorezone development can also extend into the lake littoral zone with construction of docks, revetments, riprap, often leading to destruction of littoral wetlands and macrophytes.

The habitat experienced by aquatic organisms consists of the water and the substrate, including structure and constituent chemicals. For the purposes of this protocol, water quality is a component of habitat. In-lake habitat includes both the physical and chemical environment experienced by the biota, and is, in turn, influenced by the watershed through runoff and loadings. Habitat measurement seeks to identify the physical and chemical characteristics of the lake habitat - both natural and anthropogenic - that affect the biota of the lake.

Habitat measurement, consisting of both watershed and in-lake observations, has two purposes. First, it helps in placing a lake into a category determined by a classification scheme. Second, it can help identify anthropogenic disturbances and exposure that might be responsible for biological degradation. Habitat measurement thus comprises two kinds of variables:

Classification variables - Those attributes intrinsic to the system and relatively unaffected by human activities (e.g., geology, soils, lake and watershed morphology).

Assessment variables - Those attributes which either are direct measures of human activity (e.g., land use, discharges) or are influenced by human activity (e.g., most water quality variables).

The classification variables are those which are not affected by human influence, and are primarily measures of the morphology and geology of the lake and watershed. The classification variables assist in placing the lake into one of the categories for which reference conditions have been determined. It is then possible to determine the deviation of conditions in the test lake from reference conditions, for both habitat and biological indicators.

Several habitat parameters are obtained or estimated from existing sources of information such as maps and Geographic Information Systems (GIS). The parameters include lake area, depth, shoreline length, watershed area, watershed slope, soil types, geology, and watershed land use.

The habitat measurement component of the field sampling program consists of in-lake physical and chemical measurements, as well as a shorezone habitat survey. The shorezone survey is based on the Environmental Monitoring and Assessment Program (EMAP) lake habitat assessment (USEPA 1994a, USEPA 1994b, USEPA 1993a).

5.1 Watershed Habitat

5.1.1 Measurements

The purpose of examining watershed parameters is to assist in classifying a lake and to determine whether watershed conditions might account for observed biological status. A number of human practices in lake watersheds affect lake habitat through sediment loading, nutrient loading, contaminant loading, hydrologic changes, and direct habitat alteration (e.g., removal of wetlands). Any one human activity can influence several loading rates. For example, livestock management practices can affect both nutrient and sediment loads. Watershed parameters include both classification and assessment variables (Table 5-1). Most measures of morphology and land use can be obtained from USGS, state, or county data bases.

5.1.2 Watershed Metrics

Discharges - Data from permitted discharges can be used to develop direct estimates of point-source loadings into receiving waters, and they take into account the effects of sewage diversions and implemented control technologies. However, discharges cannot account for nonpoint sources.

Watershed Area - The quantity of runoff entering a lake is directly affected by the lakes watershed area. The ratio of lake watershed area to lake surface area affects sediment and nutrient loadings and retention time. Reservoirs with a small ratio are better able to support sport fish populations (Hill 1986). The ratio is especially important for reservoirs and flowage lakes, where its value can vary widely.

Land Use - Water quality, especially nutrient concentrations and turbidity, is strongly associated with land use. The most important land use variables are urban, agricultural, and forest land use, as percent of the watershed area. Also important is watershed road density (length per area), which can be an excellent predictor of trophic variables and chloride concentration (USEPA 1993a). More detailed breakdowns of land use classes (e.g., high-density urban, transportation, pasture, row crops, etc.) can be estimated for diagnostic investigation.

A detailed nonpoint source evaluation might be called for if more than one land use type appears to be a probable cause for impairment. A standard screening procedure (Schueler 1987) can be applied to estimate sediments, nutrients, and contaminants from both urban and nonurban sources. The screening procedure allows identification of the primary likely sources of impairment and hence a preliminary ranking of potential sources.

The land use variables are tabulated on a watershed-wide basis. This approach does not take into account the effects of distance from the receiving waters, riparian buffers, or best management practices (BMPs). Runoff and pollution of surface waters from agricultural land are highly variable, depending on slope, soil erosivity, tillage practices, distribution of rainfall, and the presence of riparian buffers and hedgerows (Schueler 1987). Taking into account riparian buffers and BMPs, together with other watershed influences, would require a comprehensive runoff and loading model, and is beyond the scope of this guidance.

Population Density and Related Measurements - Nonagricultural pollution is the product of people and their activities; hence, population density is an excellent predictor of pollutant loadings. Population density is also strongly correlated with urban land use and discharges; therefore, simultaneous assessment with these collinear variables should be done with caution. Population density might be a more accurate indicator of total human activity than is land use, because population estimates are updated more frequently than land use data. The variables that most directly affect lake quality are discharges and the watershed impervious area. Nevertheless, population density may be a better single measurement.

5.2 In-lake Habitat

5.2.1 Measurements

Physical-chemical habitat measurement comprises several common measures of lake water quality and can point to water quality problems that are not observable at the coarser resolution of the entire watershed. It can also provide additional evidence for potential causes identified from the watershed or shoreline assessment. Physical and chemical parameters and the measurements derived from them are listed in Table 5-2.

Secchi Depth - Secchi depth, which has a long history as a lake assessment variable, is a simple and reliable measure of light transmittance and turbidity. It is used in various trophic indices, including Carlson’s Trophic State Index (TSI) (Carlson 1977).

Nutrients - Water quality measurements can form the basis of several measurements (Table 5-2). Total phosphorus concentration forms part of Carlson’s TSI (Carlson 1977) and is an important predictor of lake productivity in north temperate lakes (Vollenweider 1975). The nitrogen-to-phosphorus (N:P) ratio is used to predict the likelihood of cyanobacteria blooms (e.g., Smith 1983). Calculation of trophic state indices is given in Section 7.2.3.

Dissolved Oxygen - Dissolved oxygen (DO) is necessary for aquatic life, and most state water quality regulations include a standard for dissolved oxygen, usually expressed as the maximum amount of time that DO is allowed to fall below a critical value (typically 4 or 5mg/L). Several measurements have been developed for DO, including:

• Index period DO measurement near bottom of lake.
• Depth from the surface at which DO falls below a threshold value (oxycline) (Scott et al. 1991).
• Annual or seasonal minimum value in hypolimnion or epilimnion.
• Annual or seasonal mean value in hypolimnion or epilimnion.
• Annual or seasonal percent time below a threshold DO value at the bottom of the lake (USEPA 1993a).
• Annual or seasonal mean water volume or percent of total volume below a threshold DO value (Dycus and Meinert 1992).

The first 2 measurements require only a single DO profile. Depth of the oxycline might be the most useful single-point DO measurement of a waterbody (Scott et al. 1991), provided that the observation is made when hypoxia is at its maximum annual extent (usually late summer). The remaining 4 measurements all require regular observations during a year or an index season. In general, estimates of time or volume below a threshold value are more precise and accurate than estimates of minimum values (USEPA 1993a).

5.3 Shorezone and Littoral Habitat

5.3.1 Measurements

The shorezone habitat assessment is important for identifying potential causes of impairment because many lakes are impacted by development and land use on the shore. Because the lakeshore is the part of the watershed closest to the lake, shorezone land use has the largest potential impact on lake biological integrity. The shorezone assessment procedure is the same as that for watershed evaluation: shorezone habitat variables are compared to reference conditions and, if significantly different, are identified as probable causes of biological impairment.

EMAP Surface Waters has developed an extensive shorezone and littoral survey methodology to characterize riparian and littoral habitat (USEPA 1994a, USEPA 1993a, USEPA 1991e). The index period is late summer when vegetation is at its annual maximum. The riparian characterization consists of estimates of dominance of vegetation in canopy, understory, and groundcover; substrate type; bank angle; and dominance of human features (buildings, lawns, cultivation, etc.). Littoral characterization is done at a 10m distance from shore and includes depth, surface film, substrate, macrophyte cover, fish cover, and a summary habitat classification (USEPA 1993a). The shore of each lake is surveyed at 10 sites, and the frequency of disturbance is estimated for each lake from the survey data.

The shorezone and littoral assessment for lake biological surveys presented here is a modification of the EMAP shorezone assessment (Table 5-3) (USEPA 1994a).

5.3.2 Shorezone Metrics

Most shorezone measurements are means of the littoral and shorezone habitat metric values. The shorezone and littoral cover measurements are expressed as the mean of the values of all transects. The human influence measurements are different because they are based on presence or absence observations within the transects.

These measurements are weighted, with each present observation receiving a score of 1 and each “adjacent” observation receiving a score of 1/2. The human influence score in each category is the mean of all transects. It is in the range of 0-1, with 0 reflecting no influence and 1 indicating that the influence (e.g., buildings) was found in every transect.

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Chapter 7 ~ Chapter 8 ~ Chapter 9 ~ Chapter 10
Appendix A ~ Appendix B ~ Appendix C ~ Appendix D
Appendix E ~ Appendix F ~ Appendix G

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