Water Quality in Peñasquitos Creek and Lagoon: A Surprising History of Deliberate Pollution

by Mike Kelly

[Major parts of this article are reprinted from my article of February 1998 for the Earth Times and from our own Canyon News.]

Why is the water quality of Peñasquitos Creek now “fair” when tested? At one time it was “poor” to “toxic.” Before Mira Mesa or Rancho Penasquitos or much of Carmel Valley were developed, various municipalities decided the best way to deal with the sewage from the already developed areas was to dump it into our waterways, especially Peñasquitos Creek and Peñasquitos Lagoon. They built treatment facilities where the raw sewage was either dumped by truck or pumped by pipelines. There it was treated in most, not all, cases to a certain level they called an effluent. It was not potable water quality. You wouldn’t want to drink it or bath or swim in it. It was then pumped into our creek and the lagoon historically. How historically? Before the details of where and when, let’s set the stage for how some of this pumping would be affected by the local landscape, in this case, Peñasquitos Lagoon.

A brief history: a creek by any other name ...

Sorrento Valley and Sorrento Creek are new names. Until the 1960s, they were Soledad Valley and Soledad Creek. There is still a Soledad Canyon in the southern (upper) portion of Sorrento Valley. It is now only a major finger canyon, running northwest to southeast off Carroll Canyon, carrying the Santa Fe Railroad under Miramar Road and across the Marine Corp Air Station. It’s a beautiful canyon, with some of San Diego’s oldest coast live oaks, good habitat, mule deer, hawks, etc. It’s also a good wildlife corridor. You can access it off of Carroll Road at Scranton. Peñasquitos Creek once referred to the entire length of the creek, from the foothills of Poway all the way into Soledad Valley. Now, the upper portion in Poway is called Poway Creek.

Watersheds

Webster’s defines “watershed” as “the area drained by a river or river system”. The watershed that drains into Peñasquitos Lagoon ranges from 95 sq. mi. (ACOE, 1967) to 98 sq. mi. (Prestegaard 1975), depending on whose estimate you use. It includes the drainages of Carmel Valley, Carroll Canyon, and Peñasquitos Canyon (Peñasquitos Canyon reaches all the way up into Poway).

The Peñasquitos drainage or sub-watershed is the largest of the three, being about 58 sq. mi. The major creeks or tributaries flowing in these drainages include Deer Canyon Creek, which flows into Carmel Creek in Carmel Valley; Carroll Creek; Pomerado, Rattlesnake, and Beeler Creeks which all flow into Poway Creek, which becomes Peñasquitos Creek and Chicarita Creek which flows into Peñasquitos Creek. Then there’s an unnamed creek flowing out of the canyon we call Darkwood running north to south into our creek. It’s spring fed and is year-round at this time.

The insults begin

I use insults here as both a technical term for negative impacts on the land and water, and as a pejorative. The first major insult to Peñasquitos Lagoon occurred with the building of the railroad in about 1888. This began the process of closing the lagoon mouth to the influence of the tides that are necessary to maintain it as a healthy salt water-dominated water and marsh habitat.

Ellis and Lee reported in 1919 that the “Soledad Streams” were able to keep narrow channels open through the beach, at least during part of the year. However, the building of Highway 101 across the lagoon in 1932 worsened the situation. The lagoon began to be closed most of the time, causing a die-off of saltwater- dependent organisms and vegetation and a shift in the types of vegetation present. For example, no living mollusk species were found in several studies in the 1960s. Only during exceptionally wet winters could sufficient freshwater collect to break through the barrier bar that develops in the lagoon mouth.

Sewage flows in creek and lagoon

In the 1980s, our daily paper often treated us to news of sewage spills from the infamous pump station 65 in Peñasquitos Lagoon, closing beaches and promoting organism die-offs. However, what most people don’t know is that treated sewage (the PR term is “effluent”) was intentionally pumped into the Lagoon for decades.

The Callan Treatment plant, an old WWII facility located on Torrey Pines Mesa, was reactivated in 1952 and began pumping 50,000 gallons of treated effluent per day into Soledad Creek and the lagoon. It was joined in 1962 by the Sorrento plant, which was pumping about 500,000 gallons per day into the same lagoon. Another facility, the Pomerado Waste Water Treatment Plant, pumped even more treated sewage into Peñasquitos Creek from 1962 to 1972. By the way, this latter facility was owned by Poway on land leased from San Diego and located near the junction of the current Sabre Springs Parkway and Springwater Point in San Diego. In the 1980s you could still see the buildings onsite. With Republican 5th District Councilwoman Barbara Warden’s leadership, mitigation monies owed by a developer were used to take down this infrastructure and restore native habitat in the 1990s.

In addition, the Peñasquitos Settling Ponds were used for sewage treatment, perhaps as late as 1967; I have yet to find a good report on these. These ponds may still be seen, vegetated now, just west of the Rancho Santa Maria ranch house off Black Mountain Road. These 14 acres of dikes and ponds sit right next to Peñasquitos Creek. What we don’t yet know is if any of this effluent was pumped or leaked into the creek.

Likely it was since there was a constant supply of sewage trucked in by the City of Poway, if I’m correct. The old dikes and ponding areas are still there. This is an area the Friends hope to restore eventually. Many folks living downstream during this period had no idea the stream they were visiting and their kids were playing in was in large part treated sewage!

“ Effluent” impacts on lagoon

The discharge of treated effluent brought two problems with it. One was fresh water flows into the lagoon that were way above the historic levels, particularly outside of the rainy season. This effluent flow occurred during a time when urbanization was also adding fresh water to the system, not just during storm events, but all year long due to irrigation runoff.

The second problem was the high nitrate and phosphate levels of the effluent. This combination of additional nutrient-rich fresh water pouring into a closed lagoon system without adequate tidal flushing led to repeated die-offs and the shift in vegetation types. It wasn’t uncommon to see dead fish floating on the surface or on the shore. Elevated temperatures occur up in the waters of a closed system like this, and contribute to the die-offs. Such a die-off occurred in San Elijo Lagoon in the summer of 1997.

Dead fish in Los Peñasquitos Lagoon following an extended inlet closure in 2013.

Photos by Mike Hastings, Los Peñasquitos Lagoon Foundation

Another problem caused by this infusion of effluent was a tremendous mosquito problem. This prompted significant public opposition to these flows and, combined with studies of the negative biological impacts, led the Regional Water Quality Control Board to oppose continuation of these existing facilities or the building of new ones. Peñasquitos Lagoon’s mouth is now kept open with periodic and expensive bulldozing that accomplishes its purpose of permitting tidal flushing.

Urbanization has a big impact on a watershed. As you convert natural lands or agricultural lands to rooftops, parking lots and streets (impervious surfaces), you reduce the capacity of a watershed to absorb water. The resulting runoff is carried via storm drains into our canyons, not into our sewer system and safely out to the ocean as many people assume. As urbanization progresses, the water flow into the canyons far exceeds historic levels.

Runoff pollution or “urban drool” as some of us like to call it from development ringing the Preserve reduces our water quality to “fair” in water quality testing the Friends and various agencies have conducted. For instance, too many nutrients and too much nitrogen and phosphorus in the water promotes a buildup of algae and “algal blooms” to the detriment of fish and benthic organisms.

This situation is exacerbated by the inadequate tidal flushing in the lagoon, due to the closing of the mouth of the lagoon by various highways and bridges crossing it. With the mouth closed and too many nutrients and consequent algal blooms the lagoon can quickly deplete its oxygen, leading to kill-offs of its fish and mollusk populations. This, in turn, affects the bird populations that depend on the lagoon for their food.

Urbanization also means more fresh water all year, as well as during storm events, leading to a buildup of freshwater habitat at the expense of salt marsh in Peñasquitos Lagoon. Salt marsh habitat is rarer and is a priority for preservation.

Plans for an SDGE Nuclear Power Plant (!) in Sorrento Valley were finally abandoned. The proposed site was in Peñasquitos Lagoon. I believe the land has since been donated to Torrey Pines State Park. But some agencies couldn’t walk away from an old idea. The San Diego Metropolitan Wastewater Dep. proposed, in a 1980s document I have, a new Pomerado Water Reclamation Plant with live stream discharge. Both were discarded. Public opposition played a big role in both decisions.

Impacts on Peñasquitos Creek

Peñasquitos Creek is now a perennial creek, flowing year-round. Was this always the case? Firsthand observations by various individuals, plus U.S. Geological Survey data for the creek starting in 1964, indicate that the creek wasn’t consistently perennial. In years with above average rainfalls, heavy late seasonal rainfalls or significant summer rain, the creek flowed to the lagoon throughout the year. During years of average to low rain flows, certainly during periods of extended drought, it was seasonal. This shouldn’t be surprising in our arid climate. When I first moved into Mira Mesa there was no Black Mountain Road bridge. It was an at grade crossing over the creek. And during late summer months it was often dry there!

The flow data we do have (on the web at USGS) illustrates the impact of the live stream discharge between 1962-1972. From 1965-1972, the median discharge of treated effluent was .90 cfs (cubic feet per second), ranging from a low of .03 cfs to a high of 3.50 cfs. It also showed a sharp drop when the plant closed in 1972. From 1973-1979, the median discharge dropped to a low of 0.10 cfs, with a range of 0.00 to 25 cfs. In other words, at times, there was no measurable flow in the creek. Thereafter, the median discharge steadily increased, even during the summer months, probably reflecting increased runoff due to urbanization in the watershed.

The natural springs feeding Peñasquitos Creek are too few and far between to promote a year-round flow, except in their immediate downstream areas. The largest natural spring pumps up to 86,000 gallons per day into the creek. If you were standing downstream of one of these springs, the creek would certainly be flowing past you at any given time, probably, but not all the way to the ocean. If you were standing downstream in the lagoon during the period of 1950- 1972, you would have been seeing a flow but mostly of treated effluent.

Now, however, we have a strong year-round flow, even during the most recent drought, due to irrigation, car washing, etc. Is this additional flow good or bad? These flows do tend to bring toxics oil from driveways, pesticides and fertilizer all harmful to some extent to the water and the organisms in it.

However, each signficant finger canyon in the Preserve now has a new riparian area in it: this is both good and bad. Riparian areas in the desert tend to be scarce, but extremely important to wildlife. Adding some small acreages is beneficial. On the negative side, this same runoff brings seeds of exotic plants, which tend to have a negative impact on local flora and fauna. The Friends are spending considerable energies clearing these exotics out of these same canyons. Constant management can control the exotics.

The worst impact from urbanization, I feel, is the increase in peak flow and velocity during storms. We are seeing much more erosion, areas that are denuded and remain so, and beds of cobble or bedrock with no vegetation, especially in Lopez Canyon. The Friends are still grappling with how to mitigate this problem.

Fishing in the Preserve: safe to eat?

Did you know that it’s legal to fish in the Preserve if you have a valid fishing license? People use to fish and had their favorite fishing holes. Not so much today, probably because there are Rangers patrolling and they don’t have licenses? They were after our large-mouth bass. But, given the pollution, were they safe to eat? Answer, probably. The State of California asked our cooperation in a carcinogen study they do every so often on every stream in the state I think. Would we catch some of our fish and send them up to them for study. Our Will Bowen eagerly volunteered to do this and later we got the results. No carcinogens in our fish.

Are mining tailings a pollution problem?

If you explore the south side of Peñasquitos Creek in Sabre Springs you soon come to a series of small “hills” or a ridge next to the creek. They look unnatural and it turns out they are. They’re piles of mining tailings. There’s a little known mine in the hills above Sabre Springs south I’ve visited. I can’t find information about it on line, except a vague reference it might have been “Mine 3.” I believe it was for granite, but that’s just a guess. The significance is that tailings from the mine were piled right next to the creek. Why? Why not pile them up nearer the mine itself. Was the creek itself somehow being used to process something?