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Flow alteration is computed for each river segment and expressed as the deviation of developed-condition flows from baseline-condition flows, using a small set of flow metrics that are strongly linked to ecological conditions and are amenable to water management.


The objective of this step in the ELOHA framework, as depicted in the flow chart, is to create a database, ideally in a GIS, of stream segments that looks something like the figure below.  Each segment's "analysis node" is assigned a river type (bold font) and measures of hydrologic alteration (normal font). 

To assess the degree of flow alteration at each analysis node, baseline hydrology is compared to current hydrology stored in the hydrologic foundation database.  This step serves two purposes.  First, it standardizes hydrologic impacts, allowing creation of a degree-of-alteration data set to use in combination with ecological data from multiple rivers.  This enables data from individual river segments to be combined to define flow-ecology relationships for river types.  Second, it helps scientists and stakeholders understand the degree to which streamflow has already been altered throughout the region. 
Hydrologic characteristics describe the magnitude, timing, frequency, duration, and rate of change of streamflow, ground water, or lake levels.  The first step in assessing hydrologic alteration is to select streamflow metrics that describe these characteristics and are ecologically relevant and practical for making water management decisions  (Mathews and Richter, 2007).  Kennard et al (2009) provide guidance for estimating flow metrics for ecological studies. Weiskel et al (2010) developed indicators to characterize various types of potential alteration, including water withdrawals, treated wastewater discharges, construction of onsite septic systems and dams, forest clearing, and urbanization for subbasins and groundwater contributing areas in Massachusetts. Gao et al (2009) developed a small set of independent and representative hydrologic indicators to best characterize hydrologic alteration caused by reservoirs and other forms of river regulation, and found that "ecodeficit" and "ecosurplus" provide good overall representation of the degree of alteration of a streamflow time series.
Even where scientists are beginning to understand how ecological systems depend on streamflow patterns, they often describe these patterns in terms of hydrologic statistics that are difficult to apply to water management.  To regulate water use, water managers need the allowable volumes or levels of water withdrawals at different times of the year.  To manage reservoirs, operators need volumetric dam release requirements at different times of the year.  Scientists and water managers must work closely together from the inception of ELOHA applications to ensure that scientists analyze flow metrics that water managers can use to mimic, to the extent possible, natural flow patterns. Notice in the figure above that each river type may use a different set of metrics for this analysis. 
 Computer Programs
Several software packages are capable of computing flow alteration, using daily streamflow data as input. New Jersey, Massachusetts, and Missouri used the Hydrologic Alteration Tool (HAT) software in the U.S. Geological Survey's Hydroecological Integrity Process (HIP) package to calculate flow alteration for analysis nodes with measured streamflow gauging data.  The Nature Conservancy's Indicators of Hydrologic Alteration (IHA) software also analyzes flow alteration.  In addition to traditional hydrologic metrics, IHA calculates 34 Environmental Flow Components, which were specifically developed to be ecologically relevant; amendable to water resource management; and intuitive to hydrologists, ecologists, and stakeholders alike (Richter et al. 1996; Mathews and Richter 2007). 
Hydroecological Integrity Assessment Process:  USGS HIP
Inticators of Hydrologic Alteration: TNC IHA