San Joaquin Basin

Calaveras River

Environmental Data


The Calaveras River, a tributary to the San Joaquin River, serves as an important source of water for agricultural and municipal uses in Calaveras and San Joaquin counties. In addition, the Stockton East Water District’s (SEWD) management of the river on behalf of their constituents and Calaveras County Water District (CCWD) over the past thirty years has created conditions that maintain a healthy and abundant resident rainbow trout (Oncorhynchus mykiss) fishery. While very few studies of the fishery resources in the Calaveras River have been conducted to date, SEWD’s recent monitoring indicates that steelhead, a form of rainbow trout, opportunistically use the watershed when sufficient rainfall produces passage flows in the system.

Today, although the duration and magnitude of peak winter/spring flows have been reduced due to reservoir operations, salmonids are able to opportunistically access the reach between Bellota and New Hogan for spawning whenever adequate naturally occurring migration flows are available and no structural barriers are installed (i.e., flashboard dams). Upstream and downstream migration opportunities are currently limited to occasions between November and early April when passage conditions are created by substantial precipitation events that result in flood control releases and/or run-off events below the dam. In many years, precipitation events resulting in passage conditions do not begin until December because rainfall from initial storm events is generally absorbed into the ground through infiltration and run-off does not occur until the ground becomes saturated.

Fisheries Monitoring

Fisheries monitoring has been conducted since 2002 in order to improve our understanding of salmonids, particularly O. mykiss, within the Calaveras River. Different sampling methods (e.g., RST, snorkeling, PIT tag) are being used to address different data gaps. Monitoring information will be used to assist water management decisions on the Calaveras River so that a balanced management approach is achievable. It will also be used to evaluate the effectiveness of implementing various conservation strategies.

Migration Monitoring

Since 2002, a salmonid migration monitoring program aimed at providing juvenile emigration indices (using a rotary screw trap) has been conducted to document baseline data regarding juvenile salmonid presence, abundance, and migration behavior, as well as identify the environmental and/or water management conditions that effect juvenile salmonids ability to migrate successfully out of the river and susceptibility to entrainment into unscreened diversions. Based on results of this study, it has become evident that additional information is necessary regarding O. mykiss migration patterns that can only be collected using a different monitoring technique (i.e., PIT Tag). Rotary screw traps can provide gross measures of migration characteristics (e.g., daily numbers, size at capture, timing), and their ability to detect fish is influenced by flow levels (e.g., trap can be washed out at high flow levels).

A rotary screw trap consists of a funnel shaped core suspended between two pontoons. The trap is positioned in the current so that water can enter the 5 ft wide funnel mouth. Water enters the funnel and strikes the internal screw core, causing the funnel to rotate. As the funnel rotates, fish are trapped in pockets of water and forced rearward into a livebox, where captured fish cannot escape.

The rotary screw trap is installed as early as November and remains in operation until as late as mid-July.

To view recently summarized data regarding juvenile migration monitoring click here. To view older summarized data, click on the archives link on the top of the page.


Currently, little data has been collected regarding the abundance, life-history preferences, and migration success of O. mykiss in the Calaveras River which makes it difficult to ascertain potential impacts on rainbow/steelhead trout resulting from various human activities and from the recently discovered introduction of New Zealand mud snail into the area. Additionally, the lack of information on migration characteristics (e.g., season, time, rate, and route), make it difficult to evaluate potential passage impediments in Mormon Slough and the Old Calaveras River. Upstream migration to spawning habitat for adults and downstream migration to the ocean for juveniles is fundamental to the survival of anadromous species such as steelhead and Chinook salmon. Therefore, evaluation and subsequent improvement of substantial passage impediments in Mormon Slough and the Old Calaveras River is necessary to minimize take of federally threatened steelhead and facilitate population recovery within the San Joaquin Basin.

A feasibility study was conducted by FISHBIO staff on the Calaveras River in 2004 using Passive Integrated Transponder (PIT) technology. During the feasibility study, FISHBIO staff developed a demonstration detection station and tested this station using a tagged dummy fish. In addition, reconnaissance surveys were conducted to determine appropriate areas for detection stations. Based on results of equipment testing during the feasibility study, reconnaissance surveys, and discussions with resource agencies, a pilot study called “Evaluation of Juvenile Oncorhynchus mykiss Migration and Life History Expression in the Calaveras River using Streamwidth Passive Integrated Transponder Technology” was implemented that currently has six fixed detection stations.

The Project goals are to: (1) evaluate numerous potential passage impediments within Mormon Slough and Old Calaveras River Channel to assist in prioritizing structural improvements for salmonid passage and provide baseline information for effectiveness monitoring, (2) identify opportunities for water management flexibility (e.g., flow management between routes) to improve juvenile salmonid passage through the lower Calaveras River, and (3) evaluate O. mykiss life history characteristics to increase our understanding of factors that influence life history expression and to determine the extent that water management flexibility (e.g. migration route management) may benefit the anadromous component of the population.

The Project objectives are to: (1) monitor passage of tagged O. mykiss with PIT tag detection devices throughout potential migration routes between tidewater and New Hogan Dam in the lower Calaveras River, (2) monitor environmental and structural variables throughout potential migration routes between tidewater and New Hogan Dam in the lower Calaveras River, and (3) determine the influence of environmental and biological variables on O. mykiss migration characteristics and life-history preferences.

The rotary screw trap at Shelton Road (RM 29) serves as the primary source of juvenile O. mykiss, since it provides a reliable source of YOY and Age 1+ juveniles displaying smolting and downstream migrating characteristics and it is located at the downstream extent of suitable rearing habitat. After processing, a portion of untagged fish greater than 100 mm will receive a PIT Tag. PIT tags will be surgically inserted into fish and the incision will be closed with a bio-adhesive. During the feasibility study, FISHBIO staff identified the benefit of reduced surgery times and excellent tag retention with bio-adhesive sutures versus silk sutures.

Fish Passage Improvement

Since 2001, SEWD has voluntarily implemented several temporary fish passage improvements including placing sandbags at road crossings to provide better depths and velocities for passage at these structures; installing a temporary Denil fish ladder at the Bellota Weir to allow fish access above the weir; installing a temporary barrier (i.e., net) at the head of the Old Calaveras River channel to prevent juveniles from entering and becoming stranded in the channel; and creating a sandbag wall on the Bellota Weir apron to direct flow into a lower fish ladder so that it would operate more effectively.

SEWD has participated with the California Department of Water Resources (DWR) during a fish passage study that is nearing completion and with CH2M Hill during a CALFED funded fish screen feasibility study that was completed in 2005.

All of these studies have been or are currently being conducted to collect information that will aid in the design and management of long-term conservation measures and adaptive management processes. SEWD and CCWD are working cooperatively with NMFS through an Endangered Species Act Section 10 consultation to improve the conditions for salmonids in the Calaveras River by including appropriate conservation measures and an adaptive management plan (AMP) as part of this Calaveras River Habitat Conservation Plan (CHCP). SEWD will continue to implement interim fish passage improvements until long-term fish passage and screening solutions are identified and put into operation.


Although the importance of the Calaveras River for steelhead production is currently unknown, SEWD and CCWD recognize the potential problems for salmonids caused by the Mormon Slough flood control channel, Old Calaveras River channel, and SEWD’s and CCWD’s facilities. SEWD and CCWD are committed to working collaboratively with resource agencies to identify specific problem areas and to develop and implement workable, cost-effective solutions that will enhance conditions for fishery production.