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Project: Evaluation of Assessment Indicators in Nonperennial Streams

Background and Objectives

Nonperennial streams comprise more than 50% of the total stream miles in California (and an even larger proportion in southern California). However, many bioassessment programs exclude nonperennial streams from their sampling programs. One reason for this exclusion is uncertainty regarding the performance of bioassessment tools (such as the Southern California Index of Biotic Integrity, IBI) as flow declines in these streams over the course of the summer. SCCWRP conducted a study of nonperennial streams in the San Diego region (including portions of San Diego, Orange, and Riverside Counties) to see how assessment tools performed during cycles of seasonal drying.

The Arroyo Seco, a nonperennial stream in Riverside County.


This project was initiated in 2005 and completed in 2012.


This study consisted of two components: a mapping component, to determine the extent of nonperennial streams in the San Diego region, and a sampling component to study changes in benthic community structure over time. For the mapping component, reconnaissance data from several monitoring programs, USGS stream gauges, and other SCCWRP studies were used to update information on stream flow in the National Hydrography Dataset (NHD).

For the sampling component, 15 nonperennial sites were selected throughout the region; five were sampled in 2008, and 10 were sampled in 2010. Most sites represent high-quality, near-reference condition with minimally developed watersheds. However, a few sites with grazing impacts were also included. At each site, benthic macroinvertebrates and physical habitat were assessed once every 2 to 3 weeks. In addition, nutrients and dissolved metals were assessed at a subset of sites.


For the mapping component, inaccuracies in the NHD were found at 55% of the assessed sites. In general, perennial streams were more common than suggested by the NHD, although mislabeled nonperennial sites were also observed. Many stream segments contained mixed portions of both perennial and nonperennial flow. In general, perennial flow was associated with urbanization, high elevations, and bedrock outcrops.

Despite the effects of nonperennial flow on benthic community structure, the Southern California IBI can be used to assess the condition of nonperennial streams. Nonperennial streams support different benthic macroinvertebrate communities from those found in perennial streams, but IBI scores for low stress sites were similar at both types of streams. Additional data may indicate if adjustments (e.g., changes in scoring thresholds or metrics) are required to apply the IBI to the full diversity of nonperennial stream types, such as streams with short flow durations. Little modification of current protocols is required in most cases, provided surface flow persists for sufficient duration to allow establishment of benthic macroinvertebrate communities.

Recommendations for future work included:

  1. Develop a flexible approach to characterize flow regimes at nonperennial sites
  2. Include nonperennial streams in routine and ambient bioassessment programs using existing sampling protocols and assessment tools
  3. Establish a program to monitor reference nonperennial streams that capture the full gradient of flow regimes under multiple climatic conditions
  4. Include assessments of hydrologic disturbances when trying to identify the causes of poor bioassessment scores


This project was conducted in collaboration with the California Department of Fish and Game and the San Diego Regional Water Quality Control Board.

For more information on Evaluation of Assessment Indicators in Nonperennial Streams, contact Raphael Mazor at (714) 755-3235.
This page was last updated on: 6/30/2014