Municipal separate storm sewer systems (MS4s) function in urbanized areas to convey flows during both wet weather (i.e., stormwater) and dry weather (i.e., urban runoff as well as subsurface sources of flow) to receiving waters. While urban stormwater is known to contain microbial and chemical pollutants, MS4 dry weather flows, or non-stormwater discharges (NSWDs), are much less studied, although they are also known to contain pollutants, especially when these flows include raw sewage. In addition, some natural NSWDs (e.g., from groundwater infiltrating MS4 pipes) are critical for aquatic habitat protection. Thus, it is important to distinguish NSWD sources to prevent non-natural flows while retaining natural waters (i.e., groundwater). Here, MS4 dry weather flows were assessed by analyzing water samples from MS4 outfalls across multiple watersheds and water provider service areas in south Orange County, CA; potential NSWD sources including sewage, recycled water, potable water, and groundwater were sampled and analyzed for their likely contributions to overall NSWDs. Geochemical and microbiological water quality indicators, as well as bacterial communities, differed across NSWDs, yet water quality within most locations did not vary significantly diurnally or by sampling date. Meanwhile, NSWD source waters had distinctly different bacterial taxa abundances and specific bacterial genera. Shared geochemical and microbial characteristics of certain sources and outfall flows suggested the contributions of sources to outfall flows. The average proportions by sources contributing to MS4 outfalls were further estimated by SourceTracker and FEAST, respectively. The results of this study highlight the use of multiple tools when assessing chemical and microbiological water quality to predict sources of NSWDs contributing to urban MS4 flows during dry weather. This information can be used to support management actions to reduce unnatural and high risk sources of dry weather drainage while preserving natural sources important to environmental health in downstream receiving waters.

Dry weather flows to municipal separate storm sewer systems (MS4s) pollute receiving streams. Quantifying sources is necessary to discern non-prohibited (groundwater), versus other, sources. We hypothesized that aquatic bacterial communities could trace MS4 source waters. To test, next generation sequencing of genes encoding 16S rRNA was coupled with bioinformatic analyses to assess source water differences, and for quantifying source proportions to Orange County, CA MS4 outfalls. Geochemical (boron, N species, total dissolved solids or TDS, and methylene blue active substances or MBAS) and microbiological (fecal indicator bacteria, and the human fecal DNA marker HF183) analytes were also measured. By SourceTracker analyses of sequence data, source water proportions in MS4 outfall samples averaged, volumetrically: 66.7% potable water, 16.3% groundwater, 11.4% recycled water, and 0.02% sewage, which correlated to relative abundances of sequences for specific bacterial genera. Estimated source contributions varied between outfalls, yet source proportions appeared stable at each outfall across multiple sampling events, except when recycled water varied diurnally with irrigation. Although sequence-based sewage proportions matched estimates based on E. coli , enterococci, and HF183, other sources were only distinguishable by sequencing. These results support that bacterial community analysis allows for differentiating dry weather flow sources to urban MS4 outfalls.

A key challenge in managing flow alteration is determining the severity and pattern of alteration associated with the degradation of biological communities. Understanding these patterns helps managers prioritize locations for restoration and flow management actions. However, the choices made about how to use these flow-ecology relationships can have profound implications on management decisions (e.g., which biological endpoints, which thresholds, which seasonal flow components to use). We describe a process for using flow-ecology relationships to prioritize management actions that 1) Represents the most relevant components of the annual hydrograph, 2) Demonstrates an appropriate level of sensitivity in order to discriminate locations to inform decision making, 3) Aims to protect multiple biological assemblages, 4) Reduces misclassification of priority areas (i.e., error of omission). Our approach is based on the functional flows approach which uses multiple flow metrics that describe the frequency, timing, magnitude, duration, and rate of change of seasonal process-based components of the annual hydrograph. Using this approach, we performed a flow-ecology analysis of regional bioassessment data, through which we determined where flow alteration impacts biology and prioritized reaches for changes in flow management to protect aquatic resources in a highly urbanized region of southern California, where managing scarce water resources leads to difficult decisions about tradeoffs that require technical information. We identified three important functional flow metrics for each of two bioassessment indices, one based on benthic macroinvertebrates, and another based on benthic algae. Based on thresholds that describe levels of alteration as well as thresholds describing the probability of achieving a healthy biological condition, we compared nine biological threshold combinations for each index. We found instances of flow alteration that impact biological condition highly variable (0–100% of subbasins) between combinations and we present a method for finding the most appropriate combination for prioritizing locations for flow management. We apply the final thresholds to the study region and propose 16 subbasins of high priority for implementing flow management and restoration. Importantly, we show that focusing on a single biological group would result in biologically altered locations being effectively ignored.

Flow alteration is a pervasive issue across highly urbanized watersheds that can impact the physical and biological condition of streams. In highly altered systems, flows may support novel ecosystems that may not have been found under natural conditions and reference-based environmental flow targets may not be relevant. Moreover, stream impairments such as altered channel morphology may make reference-based environmental flow targets less effective in supporting ecosystem functions. Here, we develop an approach for determining ecological flow needs in highly modified systems to support existing ecological uses utilizing the California Environmental Flows Framework (CEFF). CEFF was established to provide guidance on developing environmental flow recommendations across California’s diverse physical landscape and broad array of management contexts. This paper illustrates the application of CEFF in informing ecologically-based flow restoration in a highly altered region of South Orange County, California. The steps of CEFF were implemented including a stakeholder process to establish goals and provide input throughout the project; identifying the natural ranges of functional flow metrics, or distinct components of the natural flow regime that support ecosystem functions; refining ecological flow needs to account for altered channel morphology and the life history needs of riparian and fish species; and assessing flow alteration to inform management strategies. Key considerations and lessons learned are discussed in the context of developing ecological flow needs in highly altered systems including when non-flow related management actions (i.e., channel rehabilitation) are necessary to achieve ecological goals.