Document Sample



The Tijuana Estuary contains some of the most valued salt marsh habitat remaining in
Southern California. It is both a National Estuarine Research Reserve (NERR) and a National
Wildlife Refuge for endangered species. Located in southern San Diego County, the estuary
receives waters from a 1,700 square-mile watershed, three-quarters of which is located in
Mexico. The natural balance of fresh and salt water flows into the Tijuana Estuary has been
dramatically altered by the damming of approximately 80 percent of the runoff from Mexico,
U.S. water importation and release, wastewater discharges, groundwater extraction, and
extensive urbanization (i.e., increased runoff and wastewater discharge). These watershed
changes have the potential to increase the frequency, extent, and duration of brackish water
conditions within the estuary and impact estuarine biota, including endangered species.

Previous hydrologic studies of the estuary have focused on either the surface water flows or
the groundwater basin but have not integrated the two hydrologic components. Prior field
studies of the relationship between surface water inflows and salinity have been conducted
by Pacific Estuarine Research Laboratory (PERL). These activities included discrete
measurements of surface water salinity, temperature, and dissolved oxygen at selected
locations through the estuary. PERL conducted continuous surface water quality monitoring
at two estuarine stations, but did not have the equipment needed to collect water level or
groundwater data. Prior groundwater studies incorporated discrete measurements of water
level and conductivity and cited the overall lack of continuous groundwater quality data
within the Tijuana River Basin. Such limited and nonintegrated sampling of surface or
groundwater conditions provides valuable information about the state of the system, but
provides little information regarding the interaction of these components or their relative
contribution to the salinity within the estuary under different hydrologic conditions.


The purpose of this study is to simultaneously monitor the estuary, river, and groundwater to
provide more definitive information about causes and factors contributing to both long- and
short-term salinity fluctuations within the estuary. Monitoring over differing time scales
(daily, weekly, and monthly) will clarify the relationship between fluctuations in water level
and salinity due to tidal influences, storm events, and seasonal changes and pulses in the

The need for characterization of groundwater influences in Tijuana Estuary was identified in
previous monitoring and modeling studies. Salinity monitoring in the less-tidally-dominated
southern arm of the estuary have shown a three and one-half month time period in which
salinities declined from approximately 30 ppt to as low as 10 ppt. A similar lowering of
salinities in other regions of the estuary was not observed during that time period. In this
study, the monitoring of groundwater within the estuary is concentrated within this southern
area of the estuary.


Five surface water monitoring points and nine groundwater wells were installed within the
estuarine region. Monitoring probes and loggers were installed within the surface points and
groundwater wells over the time period of October 1998 to June 1999. The time periods of
monitoring records varied with the most continuous (October 1998 to April 1999) being three
surface points and least continuous being groundwater wells in which the loggers were
periodically rotated. Additional information was gathered from existing International
Boundary and Water Commission (IBWC) wells. Manual measurement of water levels and
specific conductances were made every one to two months during the monitoring period


Annual and peak rainfalls were lower than average in the 1999 water year (October 1998 to
September 1999). Precipitation data from Lindberg Field in San Diego (from the Department
of Water Resources website) show the 1998 to 1999 precipitation total of 6.5 inches to be a
relatively dry year. The average rainfall was 11.4 inches for 1990–1999. The peak monthly
rainfall for the monitoring period was lower and later than typically found in 1990–1998. The
peak monthly rainfall of 1.6 inches took place in April. For 1990 to 1998, previous peak
monthly rainfalls ranged from 1.5 to 9.1 inches and took place in January through March.

Daily rainfall information was available from October 1998 through January 1999 from the
IBWC gaging station and from Lindberg Field for the entire monitoring period (from the
National Weather Service website). Comparisons of the IBWC and Lindberg Field gage
information show a similar pattern and magnitude of rainfall and the complete record from
the Lindberg gage will be used in this report. Tabulated daily rainfall events show several
days with greater than 0.4 in of rain (12/5/98, 1/25/99, 2/4/99, 3/25/99, 4/1/99, and 4/11/99).

The IBWC maintains a river flow gage on the Tijuana River near the border. Reliable records
were only obtained for October through mid-December 1998 and March 1999. Daily rainfalls
between 0.32 and 0.46 inches in November and December produced river flows of about
seven cubic meters per second. Smaller rainfall events of 0.16 to 0.17 inches in March
produced flow rates of approximately five cubic meters per second. The largest rainfall
event, for which a concurrent river flow record was available, was 0.56 inches in late March
and produced a flow rate of approximately eight cubic meters per second. The peak daily
rainfall of 0.77 on 1/25/99 would have produced a higher flow rate. The April rain events
would have produced flows similar to those seen in December and March.


All surface monitoring points’ water levels were influenced by oceanic tides. All points
exhibit a time lag in rising water level relative to the oceanic tide. The amplitude of the
estuarine water level variations is less than the oceanic water level variations. In particular,
the low estuarine water levels are always greater than the low oceanic water levels. This
results from a more gradual decline in estuarine water levels during ebb flows and
subsequent incoming high tide flows. The Monument Bridge point, located in the southern
portion of the estuary, is isolated from the estuary mouth during period of low water due to a
topographic high in between the mouth and this monitoring point. The resulting isolated
ponded water maintains a high elevation of 0.5 m.

Water levels for all points fluctuated primarily due to tidal effects and only exceptions to
these conditions will be discussed below. Similarly, for most points, temperature fluctuated
diurnally (warming in afternoon from solar heating) and seasonally. Some effects of mixing
with cold seawater can be seen during certain times of the year upon the rising tide

In the Tijuana River Channel, water levels fluctuated due to tidal effects with some influence
from river flow. Salinities typically fluctuate between 35 ppt and 15 ppt depending on tidal
conditions. Periods of much lower salinities (three to seven ppt) appear to be related to
periods of rainfall (late November through early December, late January through early
February, mid-March and much of April). After rainfall, the salinities are lowered below four
ppt during low tides while high tides raise the salinities to sea water levels. Depending on the
extent of the rainfall, the lowered salinities at low tide remain for between four and six tidal
cycles. The low salinities are more persistent when they coincide with a period of low tidal

The Oneonta Slough monitoring point, located just north of the estuary inlet, has low salinity
fluctuations under low river flow conditions (+/- three ppt). The salinity is affected by
rainfall/river flow events with salinities lowered below 10 ppt during the January and
February rains and to 15 ppt during the spring rains. A relatively high rainfall/river flow
event will lower salinities between 15 and 25 ppt for two days during low tides. However, a
smaller rainfall/river flow event can lower salinities continuously for a longer period of time
during a period of low tidal fluctuations.

The South Channel monitoring point, located in a side channel just south of the main Tijuana
River Channel, is less influenced by river flow. Salinity decreases during low tides are to
values higher than 20 ppt but greater declines are seen during rainfall/high river flow events.
During the wet season, the relatively low rainfall/river flow events did not significantly
decrease salinities during periods of high tidal fluctuation. During higher rainfall/river flow
events or during moderate rainfall and low tidal fluctuations, salinities are decreased
significantly although for only one day.

Monitoring of the extreme southern channel at Monument Bridge exhibited the highest range
of salinities. During low tides, a high channel water elevation is maintained due to a
topographic high limiting ebb flow. The isolation of this channel from continual tidal

flushing has resulted in high salinities between 40 and 50 ppt for long periods of time.
Salinities are lowered to 20 ppt and less than one ppt during some rainfall/high river flow
events. The dry season record shows the high salinities of 40 ppt produced by evaporation
occurring during times of low water elevation. As high tides breach the topographic high
isolating the southern channel, the channel salinities decrease. Rainfall events of equal
magnitudes (0.16–0.17 in) which occurred in mid-March caused very different salinity
responses at this location. A slight increase in water elevation and decrease in salinity occurs
for the 3/11 rainfall while the 3/15 rainfall increases water elevation by at least two meters
and decreases salinities to below three ppt for two days. A very strong decrease in salinity to
one ppt over two days and tidal cycles occurred with the 4/1 rainfall of 0.59 inches. The
variable response of salinities and water elevations in this extreme southern channel could be
the result of flow from the southern valleys of Goat Canyon and Smuggler’s Gulch which
funnel runoff directly from the western Tijuana area to the southern estuary.


Contours of groundwater elevation and salinity for the entire Tijuana River Valley and
Estuary indicate little variation over the monitoring period. The groundwater hydraulic
gradient indicates westward flow down the valley with an overall gradient of 0.0016 to
0.0020. The contour pattern is similar to those previously published in earlier reports but
extends groundwater elevation information to the west. The hydraulic gradient in the vicinity
of the estuarine channels decreases but the elevations are still above mean sea level. As
expected, salinities are generally higher in wells closer to the ocean. Salinities in the inland
IBWC wells are typically less than three ppt with the exception of two wells. These two
wells exhibit anomalously high salinities of 5.8 to 6.5 ppt and are probably impacted by local
irrigation and fertilizer application.

Within the estuarine region, the salinity pattern is impacted by the high salinities found in
some shallow wells and the two southernmost wells. The shallow hand-augered wells
extended to a depth of seven feet and were completed in finer grained sediments. The two
southernmost wells were completed in very fine silt and clay and are also in regions of
shallow depressions and possible stagnant water. The distribution of lagoon muds and
decreased hydraulic gradient appears to limit groundwater flow and enhance evaporative
concentration of salinities in these regions. All of these wells are within zones characterized
as salt marsh/salt panne.

With the exception of the extreme high salinity wells, groundwater salinities decreased from
sea water salinities to freshwater over a horizontal distance of 2,000 meters. The decrease in
hydraulic gradient occurs at approximately the same distance inland. Salinities within
groundwater did not fluctuate as dramatically as surface water salinities


Interactions between groundwater and estuarine water were evaluated by comparing water
level and salinity responses to rainfall events. Over one inch of rain fell on January 25 and
26, 1999, and the resulting increase in the southernmost Monument Bridge Channel water

level was maintained over several days. The decrease in salinity in the channel was more
subdued but apparent over the same time period. A gradual increase in groundwater levels
was observed with very little variation in salinities. There is not a decrease in groundwater
salinities of the same magnitude as the surface channel salinity decline. A similar pattern is
observed for subsequent rainfall events.

The much higher decrease in surface channel salinities relative to groundwater salinities
indicates influences of surface water runoff. While the groundwater flow and salinities affect
the overall long-term estuarine water levels and salinities by controlling the position of the
sea water-freshwater mixing zone, extreme declines in salinities over the period of two days
are controlled by surface stormwater runoff. The channel salinity in January and February
storms declined gradually to approximately 20 ppt over several days. Storms of similar
magnitude (0.6 in rain) in March and April induced salinity drops to zero ppt over two days.
Runoff flow patterns differed markedly between these time periods indicating possible
variations in origin of runoff or runoff flow patterns. The January and February rains appear
to have induced significant flow in the main Tijuana River Channel with river water
intruding into Oneonta Slough and the Monument Bridge Channel. The March and April
rains produced less impact in the Tijuana River and Oneonta Slough while having a much
stronger impact on the southernmost channel at Monument Bridge. The latter rains of similar
magnitude as the February rains may have produced more runoff from Goat Canyon and
Smuggler’s Gulch into the southern estuary.

This study’s intensive monitoring has shown a different pattern of salinities than prior
monthly monitoring in the southern estuary. Monthly monitoring in 1996 indicated possible
long-term lowering of salinities from two monthly data points (January and February).
Monitoring during 1999 indicated lowering of salinities for several days at the most. The
differences among the studies could be due to the increase in monitoring frequency or
differences in yearly rainfalls. Rainfall in 1996 was less than precipitation in 1999 and would
not be expected to produce longer term salinity decreases. The two monthly monitoring
points may have been sampled within two days of a rainfall event and would not have been
representative of the salinity over a longer time period.


This study represents the first intensive monitoring of multiple surface and groundwater
points in the Tijuana Estuary. The Tijuana River Monitoring Point exhibited extreme
fluctuations in salinities that were controlled by tides. Tidal fluctuations in salinities were
less extreme in three monitoring points off of the main channel (Oneonta Slough, South
Channel, and Monument Bridge Channel). However, these adjacent channels had significant
decreases in salinity over the period of several days following rainfall events. Southernmost
channels (Monument Bridge and Kiosk) were hydraulically isolated from the main estuary
during low tides and became hypersaline due to evaporative effects.

Groundwater salinities showed little temporal variation and, with the exception of “hot
spots,” showed a gradual transition or seawater-freshwater mixing zone over a distance of
2,000 meters. Within the 2,000-meter long mixing zone, the groundwater hydraulic gradient

is much lower than the hydraulic gradient inland. The presence of extensive lagoonal muds
and low hydraulic gradients produces stagnant groundwater which is hypersaline. These high
salinity groundwaters are found south along the border and in salt panne sites. Groundwater
salinities and levels exhibited little or no effects from rainfall.

The groundwater flows and salinities play an important part in the overall long-term water
levels and salinities in the estuary. The amount of groundwater flow and its salinity will
control the position of the salt water-freshwater mixing zone. The position of the mixing
zone will also affect the occurrence of hypersaline salt pannes. These areas tend to occur
within the mixing zone with its lower hydraulic gradients. Long-term flow within the Tijuana
River downstream of the IBWC gaging station is most likely maintained by groundwater.

Short-term (several days) extreme salinity variations in estuarine channels result from inflow
of storm water runoff. Differences in salinity changes with rainfalls of similar magnitude
indicate possible variations in runoff source to the southern estuary. Some rainfall events
produced extreme salinity reductions in the northern estuary and more subdued salinity
decreases in the southern estuary. This pattern could be produced by river flow intruding into
the southern channels of the estuary. Other rainfall events showed small decreases in the
vicinity of the Tijuana River but produced extreme salinity reductions in the southern
estuary. Such a pattern of salinity reduction could be a result of runoff from Smuggler’s
Gulch and Goat Canyon bypassing the main river and flowing directly into the southern