Summary The rate of microbial respiration on fine‐grained stream sediments was measured at 371 first to fourth‐order streams in the Central Appalachian region (Maryland, Pennsylvania, Virginia, and West Virginia), Southern Rocky Mountains (Colorado), and California's Central Valley in 1994 and 1995. Study streams were randomly selected from the United States Environmental Protection Agency's (USEPA) River Reach File (RF3) using the sample design developed by USEPA's Environmental Monitoring and Assessment Program (EMAP). Respiration rate ranged from 0 to 0.621 g O2 g‐1 AFDM h‐1 in Central Appalachian streams, 0‐0.254 g O2 g‐1 AFDM h‐1 in Rocky Mountain streams, and 0‐0.436 g O2 g‐1 AFDM h‐1 in Central Valley streams. Respiration was significantly lower in Southern Rocky Mountain streams and in cold water streams (< 15 °C) of the Central Appalachians. Within a defined index period, respiration was not significantly different between years, and was significantly correlated with stream temperature and chemistry (DOC, total N, total P, K, Cl, and alkalinity). The uniformity of respiration estimates among the three study regions suggests that sediment microbial respiration may be collected at any number of scales above the site‐level for reliable prediction of respiration patterns at larger spatial scales.

Pollutants can be reduced, ameliorated, or assimilated when riparian ecosystems have the vegetation, water, and soil/landform needed for riparian functions. Loss of physical form and ecological function unravels assimilation processes, increasing supply and transport of pollutants. Water quality and aquatic organisms are response measures of accumulated upstream discharges, and ultimately of changes in riparian functions. Thus, water quality monitoring often fails to identify or lags behind many causes of pollution or remediation from riparian degradation. This paper reviews the interagency riparian proper functioning condition (PFC) assessment for lotic (running water) riparian ecosystems and outlines connections between PFC and water quality attributes (sediment, nutrients, temperature, and dissolved oxygen [DO]). The PFC interaction of hydrology, vegetation, and soils/landforms influences water quality by dissipating energy associated with high waterflow, thereby reducing vertical instability and lateral erosion while developing floodplains with captured sediment and nutrients. Slowing flood water enables aquifer recharge, deposition, and plant nutrient uptake. Water-loving, densely rooted streambank stabilizing vegetation and/or wood helps integrate riparian functions to maintain channel pattern, profile, and dimension with characteristics for a diversity of habitats. A complex food web helps slow the nutrient spiral with uptake and storage. Temperature fluctuations are dampened by delayed discharges, narrower and deeper active channels, coarser substrates that enhance hyporheic interchange, and shade from riparian vegetation. After assessment and implementation, monitoring recovery of impaired riparian function attributes (e.g., streambank plant species) naturally focuses on persistent drivers of water quality and aquatic habitat. This provides timely environmental indicators of stream ecological health and water quality remediation projects or land management. Key words: environmental indicators-function-nutrients-rivers and streamssediment-temperatureWater quality standards are based on needs for beneficial uses, whereas opportunities for remediation are often based on need(s) for riparian functions. Water quality or biological community assessments (USEPA 2009a(USEPA , 2009b cannot predict if an ecosystem is crossing geomorphic or ecological thresholds causing devastating changes to the riparian and aquatic ecosystems (Hall et al. 2014;Kozlowski et al. 2013). For nonpoint source issues, water quality data are lagging indicators (response indicators) and do not inform riparian resource managers or riparian restoration monitors in a timeframe relevant for adaptive management. Water quality and many other terrestrial and aquatic ecosystem goods and services depend on riparian functions. One of the goals of many federal, state, and tribal environmental and natural resource programs is to maintain and restore functionality of stream and wetland riparian areas. This impacts sediment and nutrient loa...

Structural physical habitat attributes include indices of stream size, channel gradient, substrate size, habitat complexity, and riparian vegetation cover and structure. The Environmental Monitoring and Assessment Program (EMAP) is designed to assess the status and trends of ecological resources at different scales. High-resolution remote sensing provides unique capabilities in detecting a variety of features and indicators of environmental health and condition. LIDAR is an airborne scanning laser system that provides data on topography, channel dimensions (width, depth), slope, channel complexity (residual pools, volume, morphometric complexity, hydraulic roughness), riparian vegetation (height and density), dimensions of riparian zone, anthropogenic alterations and disturbances, and channel and riparian interaction. Hyperspectral aerial imagery offers the advantage of high spectral and spatial resolution allowing for the detection and identification of riparian vegetation and natural and anthropogenic features at a resolution not possible with satellite imagery. When combined, or fused, these technologies comprise a powerful geospatial data set for assessing and monitoring lentic and lotic environmental characteristics and condition.

Enterococci bacteria are used to indicate the presence of human and/or animal fecal materials in surface water. In addition to human influences on the quality of surface water, a cattle grazing is a widespread and persistent ecological stressor in the Western United States. Cattle may affect surface water quality directly by depositing nutrients and bacteria, and indirectly by damaging stream banks or removing vegetation cover, which may lead to increased sediment loads. This study used the State of Oregon surface water data to determine the likelihood of animal pathogen presence using enterococci and analyzed the spatial distribution and relationship of biotic (enterococci) and abiotic (nitrogen and phosphorous) surface water constituents to landscape metrics and others (e.g. human use, percent riparian cover, natural covers, grazing, etc.). We used a grazing potential index (GPI) based on proximity to water, land ownership and forage availability. Mean and variability of GPI, forage availability, stream density and length, and landscape metrics were related to enterococci and many forms of nitrogen and phosphorous in standard and logistic regression models. The GPI did not have a significant role in the models, but forage related variables had significant contribution. Urban land use within stream reach was the main driving factor when exceeding the threshold (> or =35 cfu/100 ml), agriculture was the driving force in elevating enterococci in sites where enterococci concentration was <35 cfu/100 ml. Landscape metrics related to amount of agriculture, wetlands and urban all contributed to increasing nutrients in surface water but at different scales. The probability of having sites with concentrations of enterococci above the threshold was much lower in areas of natural land cover and much higher in areas with higher urban land use within 60 m of stream. A 1% increase in natural land cover was associated with a 12% decrease in the predicted odds of having a site exceeding the threshold. Opposite to natural land cover, a one unit change in each of manmade barren and urban land use led to an increase of the likelihood of exceeding the threshold by 73%, and 11%, respectively. Change in urban land use had a higher influence on the likelihood of a site exceeding the threshold than that of natural land cover.

Prioritizing total maximum daily load (TMDL) development starts by considering the scope and severity of water pollution and risks to public health and aquatic life. Methodology using quantitative assessments of in-stream water quality is appropriate and effective for point source (PS) dominated discharge, but less so in watersheds with mostly nonpoint source (NPS) related impairments. For NPSs, prioritization in TMDL development and implementation of associated best management practices should focus on restoration of ecosystem physical functions, including how restoration effectiveness depends on design, maintenance and placement within the watershed. To refine the approach to TMDL development, regulators and stakeholders must first ask if the watershed, or ecosystem, is at risk of losing riparian or other ecologically based physical attributes and processes. If so, the next step is an assessment of the spatial arrangement of functionality with a focus on the at-risk areas that could be lost, or could, with some help, regain functions. Evaluating stream and wetland riparian function has advantages over the traditional means of water quality and biological assessments for NPS TMDL development. Understanding how an ecosystem functions enables stakeholders and regulators to determine the severity of problem(s), identify source(s) of impairment, and predict and avoid a decline in water quality. The Upper Reese River, Nevada, provides an example of water quality impairment caused by NPS pollution. In this river basin, stream and wetland riparian proper functioning condition (PFC) protocol, water quality data, and remote sensing imagery were used to identify sediment sources, transport, distribution, and its impact on water quality and aquatic resources. This study found that assessments of ecological function could be used to generate leading (early) indicators of water quality degradation for targeting pollution control measures, while traditional in-stream water quality monitoring lagged in response to the deterioration in ecological functions.