compiled by Siskiyou County  Supervisor Marcia Armstrong 7/2/09

http://www.waterboards.ca.gov/northcoast/water_issues/programs/tmdls/klamath_river/090701/Chapter_6_Implementation_Plan.pdf
Shasta River (pg 21 in display of section)
6.4.4 Shasta River
6.4.4.1 Responsible Parties
The parties responsible for meeting the Klamath TMDL allocations and targets in the Shasta River Basin are the same as those identified in the Shasta River TMDL Action
Plan.

6.4.4.2 Implementation
The Klamath River TMDL analysis found that the load reductions called for in the Shasta
River TMDL are sufficient to meet water quality standards in the Klamath River. The
Shasta River TMDL Action Plan includes a goal to increase dedicated instream cold
water flows by 45 cubic feet per second (cfs). Attainment of the Klamath River
temperature TMDL, and associated temperature standards, requires achieving the Shasta
River flow goal. The Shasta River TMDL Action Plan includes a conditional waiver of
WDRs for parties discharging to the Shasta River basin as long as they comply with the

Scott River (pg 22 in display of section)

6.4.5.2 Implementation
The Scott River TMDL Action Plan includes sediment and temperature control measures,
and it is anticipated that these measures are sufficient to meet the Klamath River TMDL
watershed-wide temperature allocations and targets and are consistent with the proposed
prohibition on the discharge of excess sediment. The Scott River TMDL recommended
that the County of Siskiyou, in cooperation with other appropriate stakeholders, study the
connection between groundwater and surface water in the Scott Valley. This study is
currently underway. Attainment of the Klamath River temperature TMDL, and
associated temperature standards, requires that this study move forward and that
appropriate management practices are implemented following the study in order to ensure
adequate flow in the Scott River.

The Klamath River TMDL assigns nutrient and organic matter allocations to the Scott
River, and the Scott River Action Plan does not include measures to control discharges of
these pollutants Measures to control discharges of nutrients and organic matter from
grazing and irrigated agriculture are discussed in the watershed-wide section of the
Klamath River TMDL implementation plan (Sections 6.5.5 and 6.5.6, respectively).
Parties conducting these activities in the Scott River basin are responsible for meeting the
Klamath River TMDL allocations and targets and will be responsible for implementing
measures to control the discharge of nutrients and organic matter consistent with the
proposed grazing and irrigated agriculture WDRs and/or conditional waivers.

(page 24 of section display)
6.5 Implementation of Allocations and Targets – Watershed-Wide
This section discusses TMDL implementation for land use activities that occur
throughout the Klamath River basin in California from nonpoint sources of pollution, and
recommends implementation measures for various responsible parties to comply with the
TMDL. The following land uses were identified as the primary nonpoint sources of
pollution in the Klamath River basin that contribute to the water quality impairments:
  Road Construction and Maintenance;
  Grazing;
  Irrigated Agriculture; and
  Timber Harvest

After summarizing the watershed-wide allocations and targets (Section 6.5.1), this
section presents watershed-wide prohibitions (Sections 6.5.2 and 6.5.3), and then
addresses implementation measures associated with road construction and maintenance
(Section 6.5.4), grazing (Section 6.5.5), irrigated agriculture (Section 6.5.6), and timber
harvest (Section 6.5.7) land use activities separately. For each of the land use activities,
the sections include an analysis of the efficacy of the current Regional Water Board
regulatory strategy along with other water quality protection efforts in the basin.
Recommendations are given for additional implementation measures staff believe to be
necessary to effectively implement the TMDL. Section 6.6 then addresses
implementation measures for all land use activities on federally managed lands.
Ultimately it is the Regional Water Board’s goal to combine as many discharge
requirements for various land use activities as comprehensively as possible into one
permitting structure. Already some parties have requested that the Regional Water Board
adopt ownership-wide WDRs for timber harvest companies operating within a large
ownership within the Klamath River basin (i.e., Green Diamond). Ownership-wide
WDRs have the advantage of being developed specifically for the lands within the
ownership, and covering all activities within that area. Regional Water Board staff may
work with companies to develop terms and conditions in the WDRs that meet TMDL
requirements. Ownership-wide WDRs can also be coordinated with the landowner’s
other management plans and policies, such as Habitat Conservation Plans (HCPs) and
Natural Community Conservation Plans (NCCPs).

For temperature, specific shade and sediment-related allocations are identified in detail
that will apply to most land use activities already regulated by a Regional Water Board
permitting mechanism or scheduled for permitting in the near future. For example, sitespecific
shade potential requirements are already required for timber harvest activity
enrolled under the timber waiver, and indirectly required through a general provision of
the timber WDR, which requires compliance with the Basin Plan. Similarly, shade
requirements will be implemented in any individual water quality certifications for
specific projects under section 401 of the Clean Water Act. Shade requirements will
apply to grazing and irrigated agriculture through the TMDL conditional waiver while the
Regional Water Board develops permits for those activities.

At this time, the Regional Water Board will not impose shade requirements on rural residential land use activities
that do not otherwise require permitting by the Regional Water Board unless the activity
is associated with another discharge of waste. Compliance with state and local
regulations, general plans, and ordinances is critical to preventing water quality impacts
from these activities (e.g. onsite wastewater treatment systems, grading and construction
that results in soil disturbances of less than one acre of total land area, and residential
pesticide and fertilizer use). The proposed prohibition on the discharge of excess
sediment (Section 6.5.2) is intended to apply to all land use activity, including residential,
unless already covered by an existing permitting mechanism.
(See page 25 for shade targets)

(excerpt) In simple terms, compliance with the shade allocation is achieved by not removing trees that provide shade to the waterbody. To
accomplish this, it is recommended that responsible parties delineate a separate
management area for riparian vegetation that has the potential to shade a waterbody, and
manage these riparian areas differently than the surrounding land. These areas are
referred to variously as a riparian management zone, streamside buffer area, or a
watershed and lake protection zone. The riparian management area should be large
enough to include any trees that have the potential to provide shade to surface waters
once they reach their site potential height. In most cases, the landowner will not be
required to actively restore riparian conditions by planting trees in order to comply with
the TMDL. However, active restoration of riparian conditions may be required in
instances where riparian vegetation has been removed and causes violation of the Basin
Plan temperature standards and the Klamath River shade allocations and targets, or where
natural vegetation is not readily becoming reestablished on its own. Regional Water
Board staff acknowledge that it may be necessary in some cases to remove some riparian
vegetation to hasten recovery towards site potential effective shade conditions.

(See page 26 for sediment)

(excerpt) 6.5.2 Watershed-wide Prohibition on the Discharge of Excess Sediment
To help achieve these watershed-wide TMDL allocations and targets, the implementation
plan includes a conditional prohibition that regulates excess sediment (waste) discharges
from human related activities. The prohibition applies to all sediment sources in the
Klamath River basin that are not regulated under a Regional Water Board adopted WDR
or waiver. The prohibition is included so that the implementation plan complies with the
State NPS Policy that requires the Regional Water Board to address all discharges of
waste that can affect water quality, including non-point sources, by using some
combination of WDRs, waivers, and/or prohibitions. This prohibition applies to land
uses that contribute to the temperature impairment through the discharge of excess
sediment. Sediment discharge sites would be regulated by this prohibition until the
Regional Water Board adopts an alternative means of regulation, such as WDRs or
waivers, as the implementation plan recommends for some categories of sediment
discharges.

(excerpt) Parties responsible for existing sediment sources must implement the following
measures.
1. Inventory: Identify sources of excess sediment discharge or threatened discharge
and quantify the discharge or threatened discharge from the sources.
2. Prioritize: Prioritize efforts to control the inventoried sediment sources based on,
but not limited to, severity of threat to water quality and beneficial uses, the
feasibility of source control, and source site accessibility.
3. Schedule: Develop a schedule to implement the cleanup of controllable sediment
discharge sites.
4. Implement: Develop and implement feasible sediment control practices to
prevent, minimize, and control the discharge.
5. Monitor and Adapt: Use monitoring results to direct adaptive management in
order to refine excess sediment control practices and implementation schedules
until discharges are reduced to a level that meets the TMDL load allocations and
water quality standards.
Landowners and land managers actively engaged in implementation of these measures
will be considered on a path towards compliance with the prohibition. In cases where
preventive or corrective action has not taken place, the Regional Water Board and/or staff
will take the appropriate enforcement measures pursuant to the Statewide Enforcement
Policy. Further, the NPS Policy allows the Regional Water Board the discretion to waive
application or enforcement of the prohibition for a particular discharge based on the
circumstances of the case.

Page 28 excerpt

6.5.3.1 Flow
Maintaining near natural flows in the Klamath River tributaries in California is an
important component of meeting the Basin Plan water temperature objective. In
particular, cold water flows are necessary to maintain the function of thermal refugia in
the Klamath River basin. Regional Water Board staff will work with other state and
federal agencies and tribes to identify and eliminate illegal diversions in the Klamath
River basin in California. In addition, Regional Water Board staff recommend that the
State Water Board staff issuing water rights permits to divert surface water in the
Klamath River basin in California consider the impact of increased diversions on
tributaries that provide thermal refugia.

Page 33 excerpt

6.5.4.3 Implementation to Address Road-Related Discharges on Private Lands
Most roads located on private lands in the Klamath River basin are associated with
timberland ownerships, however roads associated with other land uses, such as
agriculture, also exist as do a significant number of rural residential roads. In order to
comply with the TMDL, landowners are responsible for implementing effective
management practices to address nonpoint source pollution from roads on their property.
Staff recommend that sediment discharges from roads on private lands be regulated
through the proposed prohibition on discharges of excess sediment in coordination with
existing plans and programs....

Page 38 excerpt

6.5.5 Grazing
Grazing activities in the Klamath River basin have the potential to contribute to TMDL
impairments mainly through erosion, alteration of riparian functions, and discharge of
nutrients and organic matter. Grazing on nonfederal lands in California occurs mostly in
the tributary basins in the upper middle reach of the Klamath River from Scott River to
Iron Gate dam, including the Scott and Shasta River basins, and in the Lost River basin
that drains into the Klamath River in Oregon. The Regional Water Board currently does
not regulate grazing activities in the Klamath River basin, except through waivers of
WDRs adopted as part of the Scott River and Shasta River TMDL Action Plans or
through an NPDES permit if an operation is classified as a concentrated animal feeding
operation (CAFO). To control nonpoint sources of pollution from grazing activities
consistently throughout the Klamath River basin, to comply with the State NPS Policy,
and to meet the watershed-wide and tributary TMDL allocations and targets, staff
recommend the development of a Klamath River basin-wide conditional waiver of WDRs
and/or general WDRs for grazing for consideration by the Regional Water Board. A
conditional waiver of WDRs and/or general WDRs for grazing would not apply to
CAFOs already regulated through an NPDES permit. To comply with the Klamath River
watershed-wide and tributary specific load allocations and targets, any party conducting
grazing activities in the Klamath River basin must select and implement management
practices that control sediment sources, protect and maintain riparian functions, and
address discharges of nutrients and organic matter.
6.5.5.1 Responsible Parties
Any party conducting grazing activities in the Klamath River basin in California.
6.5.5.2 Implementation
Protection and Maintenance of Riparian Shade
Parties conducting grazing activities within the Klamath River basin in California are
responsible for protecting and maintaining riparian conditions that meet the riparian
shade allocation and targets. This allocation requires that riparian shade to a stream be
maintained where it exists, and that grazing activities not impede progress towards
reaching site potential effective shade conditions.
Control of Sediment Discharges
The prohibition on the discharges of excess sediment (Section 6.5.2) will apply to
sediment discharges from grazing activities until a conditional waiver of WDRs and/or
general WDRs for grazing are developed for the Klamath River basin. The prohibition as
well as a conditional waiver of WDRs and/or general WDRs for grazing will require
those responsible parties discharging sediment to survey all sediment sources on their
land and then systematically implement management practices to control those sources
pursuant to a time schedule.
Control of Nutrient and Organic Matter Discharges
To control discharges of nutrients and organic matter from animal waste deposited to
surface waters, Regional Water Board staff recommend including, as a condition of
eligibility for general WDRs or a waiver, that responsible parties implement measures to
limit livestock access to the stream channel. This recommendation is not intended to
prohibit use of surface waters for livestock watering, but rather eliminate the direct
discharge of nutrients and organic matter to surface waters in the Klamath River basin.
Ranch Water Quality Management Plans
Responsible parties shall develop a ranch management plan to organize their
implementation efforts. Ranch water quality management plans may be required as part
of the conditional waiver of WDRs and/or general WDRs for grazing and may be
required at any time by the Regional Water Board’s Executive Officer. Landowners may
choose to implement measures from an existing plan, develop their own plan, or
implement measures from a plan that is developed as a group. If an existing plan is to be
used, it is the responsibility of the landowner to ensure the plan complies with the TMDL
allocations and targets and that additional measures are included if needed. The ranch
water quality management plan should include the management practices selected by the
landowner(s) to comply with the TMDL and also include elements such as:
  A description of the existing beneficial uses to be protected from grazing
activities;
  A survey of sediment sources on the ranch, including roads, and a time schedule
for implementing measures to address those sediment sources as required by the
prohibition on the discharge of excess sediment;
  An inventory of riparian vegetation conditions, and a plan to monitor progress
towards meeting the watershed-wide riparian shade allocation and targets;
  Nutrient and organic matter control measures including limiting livestock access
to the stream channel; and
  Tracking and effectiveness monitoring of pollution control practices selected for
implementation.
Implementation Measures
Regional Water Board: Measure
  Develop general WDRs and/or a conditional waiver of WDRs for grazing activities in the Klamath River basin for Regional Water Board consideration. The waiver would require compliance with the existing TMDL load allocations in the Scott and Shasta River basins in addition to the watershed-wide temperature and nutrient allocations in the Klamath River basin.
Timeline
  December 2013
Responsible Parties-
Any party conducting grazing activities in the Klamath River basin in California: Measure
  Protect and maintain site potential effective shade conditions
Measure
  Control sources of sediment as required by the prohibition on the discharges of excess sediment and compliance with the forthcoming conditional waiver of WDRs and/or general WDRs for grazing
Measure
  Develop and implement nutrient and organic
matter control measures including limiting
livestock access to the stream channel
Measure
  Develop a ranch water quality management plan
to implement the TMDL on a prioritized
schedule or implement measures through an
existing plan.
Timeline
  1 year from USEPA adoption of the TMDL
6.5.6 Irrigated Agriculture
Activities associated with irrigated agriculture have the potential to contribute to water
quality impairments through discharges of polluted irrigation tailwater and by degrading
riparian conditions. Irrigated agriculture occurs in the Klamath River basin in California
mostly in the tributary basins in the upper middle reach of the Klamath River from Scott
River to Iron Gate dam, including the Scott and Shasta River basins, and in the Lost
River basin that drains into the Klamath River in Oregon.
6.5.6.1 Responsible Parties
Any party conducting activities associated with irrigated agriculture in the Klamath River
basin in California including irrigated pastures.
6.5.6.2 Implementation
The Regional Water Board currently does not regulate irrigated agriculture activities in
the Klamath River basin, except through waivers of WDRs adopted as part of the Scott
River and Shasta River TMDL implementation plans. To control nonpoint sources of
pollution from irrigated agriculture activities consistently throughout the Klamath River
basin in California, to comply with the State NPS Policy, and to meet the watershed-wide
and tributary TMDL allocations and targets, staff recommend the development of a
Klamath River basin-wide conditional waiver of WDRs and/or general WDRs for
irrigated agriculture for consideration by the Regional Water Board. The basin-wide
conditional waiver of WDRs and/or general WDRs for irrigated agriculture would
succeed the existing waivers in the Scott and Shasta River basins.
Staff recommend that a Klamath River basin-wide conditional waiver of WDRs and/or
general WDRs for irrigated agriculture provide landowners the option of complying with
the waiver or WDR individually or as part of a group compliance program. Group
compliance programs could be coordinated by a local RCD or other local group. As part
of a group program, the individual’s responsibility would be to implement best
management practices (BMPs) that control discharges resulting from irrigated agriculture
activities, comply with the prohibition on the discharge of excess sediment, and meet the
TMDL allocations and targets for shade, nutrients, and organic matter. Management
measures should focus on maintaining and restoring riparian vegetation, road
management to control sediment discharges, and controlling irrigation tailwater quality.
Water Quality Management Plans
Responsible parties conducting activities associated with irrigated agriculture in the
Klamath River basin shall develop water quality management plans to organize their
implementation efforts. Water quality management plans may be required as part of the
conditional waiver of WDRs and/or general WDRs for irrigated agriculture and may be
required at any time by the Regional Water Board’s Executive Officer. .Landowners
may choose to implement measures from an existing plan, develop their own plan, or
implement measures from a plan that is developed as a group. If an existing plan is to be
used, it is the responsibility of the landowner to ensure that the plan complies with the
TMDL allocations and that additional measures are included if needed. The water quality
management plan should include the management practices selected by the landowner(s)
to comply with the TMDL and may include elements such as:
  A description of the existing beneficial uses to be protected from activities associated with irrigated agriculture;
  A survey of sediment sources and a time schedule for implementing measures to address those sediment sources as required by the prohibition on the discharge of excess sediment;
  Development of a nutrient management plan to control the application of fertilizers;
  Implementation of control measures to reduce or eliminate irrigation tailwater discharges that contain elevated nutrient, organic matter, and temperature loads;
  Tracking and effectiveness monitoring of pollution control practices selected for implementation.
Implementation Measures

Regional Water Board: Measure
  Adopt WDRs and/or a conditional waiver of WDRs for activities associated with irrigated agriculture, including irrigated pastures used for grazing, by December 2012. The WDRs/waiver of WDRs will consider the existing load allocations in the Shasta and Scott River basin TMDLs and will take the place of the waivers in those basins.
Responsible Parties-
Any party conducting activities associated with irrigated agriculture in the Klamath River basin in California: Measure   Control sources of sediment as required by the prohibition on the discharge of excess sediment and forthcoming conditional waiver of WDRs and/or general WDRs for irrigated agriculture;
Measure   Implement control measures to reduce or eliminate irrigation tailwater discharges that contain elevated nutrient, organic matter, and temperature loads
Measure   Develop a water quality management plan to implement the TMDL on a prioritized schedule or implement an existing plan.