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~ (~ o ,-.) ,.j:>, '-' ""'" ( <- San Juan Seven Yea~ Research Plan WORK STATEMENT/PROTOCOL SECONDARY CHANNEL J:CHTHYOPAUNlIL CHARACTERJ:ZATJ:ON - NMGP Background: The Primary study area for this research task is the San Juan River between Shiprock, New Mexico, and Bluff, Utah. Within this reach, the river is comprised of a primary channel and frequently one or more secondary channels. Secondary channels range in length from less than 300 m to more than 3 kIn. Volume of flow in secondary channels varies from less than 0.1 m'/sec to almost equal that of the primary channel. The extent of secondary channel habitat varies with river discharge, but even at low-summer flows some secondary channel habitat is present. Some secondary channels receive inflow from ag~icultural lands, groundwater seepage, and intermittent washes. In the past 5 years, ichthyofaunal sampling has concentrated mainly upon primary channel and backwater habitats. Cursory sampling revealed that fish cOl1\ll\unities of secondary channels are different, at least qualitatively, than those of the primary channel. Non-native fishes such as red shiner (CVorinella lutrensis), fathead minnow (Pimeohales oromelas), and sunfishes (Centrarchidae) were more c=on in secondary than primary channels. Use of secondary channels by target species (Colorado squawfish, Ptvchocheiluis lucius, and roundtail chub, Gila robusta) was suspected but not confirmed until 1991 when a male Colo~ado squawfish was captured in a 3+ kIn secondary channel about 1.5 kIn upstream of its mouth. Secondary channel habitats and their use by target species need to be quantified to determine the significance of these habitats for target species in the San Juan River. Objectives: The purpose of the Secondary Channel J:chthyofaunal Characterization Study is to document species present, their relative abundance, size range (=life stage), macro-habitat associations, and seasonal-use patterns. Methods: For the purposes of this research element, a secondary channel has been tentatively defined as one which is at least 300 m in length and has flow less than 30'1' of the primary channel. This definition is arbitrary and may be modified as field investigations progress. Secondary channels are herein classified as one of four types: Type I Type II Type III Type IV = more than 1 kIn in length and less than lOt of total flow = more than 1 kIn in length and more than lOt of flow = less than 1 kIn in length and less than lOt of flow = less than 1 kIn in length and more than lOt of flow. The frequency of secondary channels varies between Ship rock and Bluff. If present, at least one will be sampled in each 8 .kIn segment of the river. Two sampling efforts will be made in 1992; the first during spring run-off and the second in late summer. In each Type I and II secondary channel sampled, fish collections, species habitat characterizations, and water quality measurements will be made at two sites. These sites will be located about one- fourth of secondary channel length from either end. One site, located about mid-channel length, will be sampled on A12