San Diego County, California

Water Quality

Water Quality Overview

Leonardo da Vinci said, “Water is the driver of nature.” Without clean and free flowing water in a naturally flowing Escondido Creek and its tributaries, the Escondido Creek watershed, including San Elijo Lagoon, will never thrive fulfill its potential to support the natural diversity of species that make our region unique.

Sadly, Escondido Creek is considered to be in poor ecological condition based on the Surface Water Ambient Monitoring Program (SWAMP) Report for the Carlsbad Watershed that was prepared for the San Diego Regional Water Quality Control Board in 2007. This was based on a combination of testing for aquatic life standards, including water chemistry, toxicity, biological assessments, and physical habitat.  Escondido Creek has suffered from multiple decades of low-level pollution from storm drain point sources, as well as periodic sewage spills and high levels of bacteria and sediments. The SWAMP Report indicates that Escondido Creek toxicity is considered low, but still evident; aquatic life is impaired; and beneficial use (such as recreation) can be compromised at beach locations due to high bacteria levels following storm events.

One indicator of stream health is called embeddedness, the degree that fine sediments surround course substrates on the surface of a stream bed. Embeddedness is important, as it provides a diversity of habitats for small animals and insects to live and reproduce. Certain species of fish, for example, need particular sizes of small gravel on which to deposit their eggs. If the gravel is not present, these fish cannot successfully reproduce. The embeddedness in Escondido Creek is considered to be poor.

While embeddedness is a good indicator of biological health, TECC has also been testing the water quality of Escondido Creek, including ammonia, alkalinity, nitrite, nitrate, phosphate, dissolved oxygen (DO), pH, and temperature. For these constituents, TECC’s data confirm the results of the SWAMP Report: ammonia and phosphate levels in the creek exceed the aquatic life standard, and nitrite exceeds the salmonid aquaculture standard.

Another indicator of stream health is the presence/absence, of macroinvertabtraes (insects) that are sensitive to pollution levels. Stoneflies (order Plecoptera) are small aquatic insects that are very sensitive to levels of pollution and that require cool, clear, well-oxygenated moving water for development of nymphs, and for that reason adults are usually found near unpolluted streams (Jewett, 1960). Stoneflies are important to stream ecology, as they serve as a food source for native fish, including steelhead. Stoneflies are found in the tributaries to Escondido Creek, but not in its main stem.

TECC Water Quality Monitoring Program

Over the years, numerous agencies and special interest groups have conducted water quality testing on various sections of Escondido Creek. Although these tests have provided useful information, they have not always been conducted at the same locations or with consistent frequency. TECC has made improving the quality of the water in Escondido Creek a priority. Fortunately, TECC has a team of active volunteers, most with water quality and/or engineering backgrounds, who have designed and implemented a routine Water Quality Monitoring Program for the Escondido Creek watershed.

The purpose of the Water Quality Monitoring Program is to establish a baseline that will be used to evaluate the condition and overall health of Escondido Creek on an ongoing basis, as well as to identify short- and long-term trends. We have been performing this monitoring since September, 2011, and now have a database that allows for meaningful evaluation of changes over time. Additional specific objectives are as follows:

  1. Determine whether any applicable water quality standards are exceeded.
  2. Evaluate inter- and intra-annual water quality cycles.
  3. Provide timely and high quality data to demonstrate the suitability of Escondido Creek for supporting a rescue hatchery for, or reintroduction of, endangered Southern Steelhead.
  4. Provide data as a service for other interested stakeholders, such as San Diego Coastkeeper.

Sampling is conducted at four locations, spanning the creek’s reach through Elfin Forest / Harmony Grove to El Camino Del Norte in the City of Encinitas. These include (from upstream to downstream): Country Club Drive; the Elfin Forest Recreational Reserve Interpretive Center; southeast of the intersection of Harmony Grove Road and Elfin Forest Road; and the bridge at El Camino Del Norte. These four sites were selected because of the relative ease in obtaining samples, their spatial location along the creek, and the fact that they are also locations that are routinely sampled by both San Diego Coastkeeper and the City of Escondido.

Water quality parameters of interest that are monitored TECC’s Water Quality Monitoring Program include the following:

  • Alkalinity
  • Ammonia
  • Dissolved Oxygen
  • Nitrate
  • Nitrite
  • pH
  • Phosphate
  • Temperature

Based on analysis of these parameters over the last four years, TECC has been able to prepare detailed spacial and temporal distributions which have clearly determined the role the natural free-flowing Escondido Creek plays in reducing water pollution levels as it flows from the City of Escondido to San Elijo Lagoon. The natural creek (as opposed to the concrete flood control channel) acts as a biofilter, removing pollutants from the stream as it progresses toward the ocean.

For example, at higher levels, nitrate enhances algae blooms. During the warmer months, algae begin to proliferate in the creek, and its growth is fueled by nitrate, which is a key nutrient. If this growth is excessive, as the algae dies and decomposes, oxygen is stripped from the water, which can be deadly to stream life. The primary source of excess nitrates in the watershed is fertilizers applied to yards, fields, and golf courses to promote plant growth. Animal waste is another source.  (Thus, you can have a direct positive impact on Escondido Creek by reducing or eliminating your use of fertilizers and picking up after your pets.) Fortunately, our testing shows that the natural processing of the creek also helps reduce nitrate levels. As the water leaves the concrete lined channel in the City of Escondido, nitrate levels are typically at their high; however, as the water advances towards the ocean, these levels decrease. Without the natural processing by the creek itself, it is more probable that detrimental algae blooms would occur more frequently in San Elijo Lagoon

In addition, as the creek passes down the 7-mile concrete channel through the City of Escondido, the water is heated significantly (up to nearly 90 oF) due to open exposure to solar radiation on the thinly spread flow. . Downstream of the concrete channel, tree and vegetation cover sustained by the creek itself, is able to greatly cool the water back to lower temperatures, which are a more conducive environment for the growth and sustainability of aquatic organisms.

From 2010 to 2015, TECC and San Diego Coastkeeper have undertaken water quality monitoring and sampling in Escondido Creek for the approximately 8-mile section of the creek extending from Harmony Grove Road at the City of Escondido Flood Control Channel to El Camino Del Norte. Four locations were tested, and based on average values (four years for TECC water quality constituents and five years for Coastkeeper bacteria sampling), the following parameters have shown significant reduction as a result of the natural in-stream attenuation:

  1. Nitrate: 71% reduction
  2. Nitrite: 94% reduction
  3. Phosphate: 17% reduction
  4. Enterococci: 39% reduction
  5. E. coli : 71% reduction
  6. Total Coliform: 39% reduction

A more detailed description of each of these parameters follows:

Descriptions of Sampled Parameters

  1. Alkalinity

The alkalinity or the buffering capacity of water refers to how well it can neutralize acidic pollution and resist changes in pH. Alkalinity measures the amount of alkaline compounds in the water, such as carbonates, bicarbonates, and hydroxides.

  1. Ammonia

Because ammonia (NH3) is rich in nitrogen, it makes an excellent fertilizer component. In fact, ammonium salts are a major source of nitrogen for commercial fertilizers. Like nitrates, ammonia may speed the process of eutrophication in waterways. Ammonia is toxic to fish and aquatic organisms, even in very low concentrations. When levels reach 0.06 mg/L, fish can suffer gill damage, and at h 0.2 mg/L, sensitive fish like trout and salmon begin to die. As levels near 2.0 mg/L, even ammonia-tolerant fish like carp begin to die. Higher pH and warmer temperatures, as well as low dissolved oxygen and carbon dioxide levels, increase the potential for ammonia toxicity. Ammonia levels greater than approximately 0.1 mg/L are generally indicative of polluted waters. The danger ammonia poses for fish depends on the water’s temperature and pH, along with the dissolved oxygen and carbon dioxide levels.

  1. Dissolved Oxygen

The concentration of dissolved oxygen (DO) in a stream is affected by temperature, flow, aquatic plants, riparian vegetation, pollution, and other factors. Streams with high DO concentrations (greater than 8 mg/L) are considered healthy and able to support a greater diversity of aquatic organisms. Such streams are typified by cooler, clear water, with enough riffles to provide sufficient mixing of atmospheric oxygen into the water. In general, DO levels less than 3 mg/L are stressful to most aquatic organisms. However, fish can move away from low DO areas. Because the temperature of the stream can vary daily, and even hourly, it is important to normalize data for the effect of temperature when analyzing the DO levels in a sample of water. This normalization is achieved by considering the saturation value. Saturation is the maximum level of DO that would be present in the water at a specific temperature, in the absence of other influences. Once the temperature of the water is known, an oxygen saturation table can be used to determine the maximum DO concentration. Percent saturation can be calculated by y dividing the measured DO result by the maximum saturation value. A healthy stream is considered to be 90-100 percent saturated. A guide for DO ranges is as follows: 0-2 mg/L: not enough oxygen to support life; 2-4 mg/L: only a few fish and aquatic insects can survive; 4-7 mg/L: good for many aquatic animals, low for cold water fish; 7-11 mg/L: very good for most stream fish.

  1. Nitrate

Nitrate (NO3) generally occurs in trace quantities in surface water. It is the essential nutrient for many photosynthetic autotrophs and has been identified as the growth-limiting nutrient. It is only found in small amounts in fresh domestic wastewater, but in effluent of nitrifying biological treatment plants, nitrate may be found in concentrations up to 30 mg-N /L. Nitrate is a less serious environmental problem, and it can be found in relatively high concentrations where it is relatively nontoxic to aquatic organisms. However, when nitrate concentrations become excessive and other essential nutrient factors are present, eutrophication and associated algal blooms can be become a problem. Natural levels of nitrate are usually less than 1 mg/L. Concentrations over 10 mg/L will have an effect on the freshwater aquatic environment. Notably, 10 mg-N/L is also the maximum concentration allowed in drinking water supplies by the United States Environmental Protection Agency. For a sensitive fish such as salmon, the recommended concentration is as low as 0.06 mg-N/L. Water with low DO may slow the rate at which ammonium is converted to nitrite and then nitrate via natural biological processes.

  1. Nitrite

Although nitrite (NO2) is extremely toxic to aquatic life, it is usually present only in trace amounts in most natural freshwater systems because it is rapidly oxidized to nitrate. Nitrites can produce a serious condition in fish called “brown blood disease” and can also react directly with hemoglobin in warm-blooded animal (including humans) to produce methemoglobin, which destroys the ability of red blood cells to transport oxygen. Nitrite levels below 0.5 mg/L seem to have no effect on warm water fish.

  1. pH

The pH is a means of expressing the hydrogen ion (H+) concentration in water and represents a measure of acidity. Mathematically, pH is the negative log of the hydrogen ion concentration, yielding a scale of 1 to 14. Solutions with lower pH values have greater hydrogen ion concentrations. Values lower than 7 are characterized as acidic, while those above 7 are considered basic; a value of precisely 7 is considered neutral. Because the pH scale is logarithmic, a one-point change indicates the strength of the acid or base has increased or decreased tenfold. pH is an important limiting chemical factor for aquatic life. If the water in a stream is too acidic or basic, the biochemical reactions of aquatic organisms may be adversely affected. Streams generally have pH values ranging between 6 and 9, depending upon the presence of dissolved substances that come from bedrock, soils, and other materials in the watershed. Changes in pH can affect water chemistry. For example, as pH increases (i.e., less acidic and more basic), smaller amounts of ammonia are toxic to fish. As pH decreases (i.e., more acidic and less basic), the concentration of metals may increase due to conditions favoring enhanced dissolution from sediments into the water.


  1. Phosphate

Small quantities of phosphorus are essential for plant growth and metabolic reactions in animals and plants. Because it is the nutrient in shortest supply in most fresh waters, even small amounts may cause significant plant growth, exerting a disproportionate influence on effected aquatic ecosystems. Phosphorus is typically introduced into waterways as phosphate (PO4-3), sources of which include animal wastes, sewage, detergent, fertilizer, and disturbed land.   Phosphate-induced algal blooms may initially increase DO via photosynthesis, but after these blooms die off more oxygen is consumed by bacteria facilitating the decomposition of decaying algal cells. Larger streams may exhibit changes due to the influence of phosphate at levels approaching 0.1 mg/L, while small streams may react at levels of 0.01 mg/L or less. Phosphates do not pose a human health risk except in very high concentrations.


  1. Temperature


Temperature is a controlling factor for aquatic life, regulating the rate of both metabolic and reproductive activities. If stream temperatures increase, decrease, or fluctuate too widely, metabolic activities may speed up, slow down, malfunction, or cease altogether. There are many factors that can influence the stream temperature. Water temperatures can fluctuate seasonally, daily, and even hourly, especially in smaller sized streams. Spring discharges and overhanging vegetation canopy provides shade, helping to insulate a stream from large temperature swings. Water temperature is also influenced by the quantity and velocity of stream flow, with larger, more swiftly flowing streams less effect by changes in air temperature and direct sunlight. Temperature affects the concentration of dissolved oxygen in a water body, with greater solubility in colder water.


TECC has an active group of volunteers that conduct water quality testing and is always looking for additional volunteers to assist with this work. In addition, TECC board members are involved in helping to improve the overall Carlsbad watershed through both involvement with the Carlsbad Watershed Network and participation on a panel evaluating the new MS4 (Municipal Separate Storm Sewer System) permit associated with the watershed’s Water Quality Improvement Plan . Additionally, TECC is promoting the implementation of changes to the concrete channel through the center of Escondido that will restore a more natural function to the creek, provide habitat restoration opportunities, and improve water quality.

If you’d like to help TECC improve the water of Escondido Creek, please contact.