Santa Ana River Native Fish Study

Problem Description

The Santa Ana Sucker was federally listed as threatened in 2000 and has been extirpated from more than 70 percent of its historical range. Within the Santa Ana River, both it and the Arroyo Chub persist in a stretch below Seven Oaks Dam where more than 65 percent of flow is treated wastewater. Researchers have proposed several explanations for the poor condition of these populations: flow regulation and reduced sediment supply below the dam, elevated water temperatures, and a growing population of non-native predators such as Largemouth Bass. Which of these matters most, and how they interact, remains unresolved.

That uncertainty has practical consequences. The Upper Santa Ana Habitat Conservation Plan depends on knowing how these populations are doing and what conditions they need, and the available data have not been sufficient to describe their distribution and status at the resolution the plan requires.

Study Questions & Objectives

This study continues annual population surveys of native and non-native fish in the Santa Ana River through 2028, using the same methods that have been applied since 2015. The resulting abundance estimates give managers a consistent long-term record of how these populations are changing.

Two lines of analysis build on that record. The first examines the non-native fish community, which has shifted substantially since surveys began. Because non-native predators show a strong negative association with the native species this survey was designed to track, understanding what drives their numbers, including removal efforts and conditions like water temperature and wastewater outflow, is necessary for interpreting what has happened to the natives.

The second asks whether native fish populations can persist over the long term, and under what conditions. Earlier work used adult survey data to estimate extirpation risk. This study extends that framework by incorporating larval fish data collected by cooperating agencies, allowing scientists to model reproduction and survival directly rather than inferring them from adult counts alone. Together the two analyses address a management question: can non-native populations be reduced enough, through removal or changes in water operations, to support native fish over time?

Study Approach

Surveys take place each September within the section of the middle Santa Ana River designated as critical habitat for the Santa Ana Sucker, roughly 16 kilometers of stream. Sampling reaches are selected using a stratified random design, which divides the river into segments based on what is known about where fish are distributed and then selects sites at random within each. Approximately 45 reaches of 50 meters each are surveyed along the main stem, with up to nine additional sites in three tributaries when time allows.

Crews work upstream through each reach using backpack electrofishing, a method that briefly stuns fish so they can be netted, measured, and returned to the water. Every fish captured is identified, weighed, and measured. At least two passes are made through each reach; a subset of reaches is enclosed with block nets and sampled three times, which lets scientists estimate how many fish the survey misses and correct the counts accordingly.

Habitat is measured in the same reaches using national protocols developed for the USGS National Water-Quality Assessment Program. Along six transects per reach, crews record water depth, velocity, channel width, streambed material, canopy cover, and features that provide cover for fish. Pairing habitat and fish data at the same locations allows scientists to examine which conditions native fish are associated with, and whether those conditions are present where the fish are not.

All survey data undergo USGS quality-assurance review and are published annually as public data releases in ScienceBase.