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An additive semi-analytic model of water clarity for the forward problem of calculating apparent optical properties (AOPs) of diffuse attenuation and Secchi depth from the inherent optical properties (IOPs) due to suspended matter in oligotrophic waters is presented. The model is general in form, taking into account algal concentration, suspended inorganic sediment concentration, particle size distribution, and dissolved organic matter to predict Secchi depth and diffuse attenuation. The model’s application to ultra-oligotrophic Lake Tahoe, California-Nevada, USA is described. The function of the clarity model is to quantify the relative effect of phytoplankton or phytoplankton-derived organic materials, other particles such as suspended mineral sediment, and dissolved organic matter on the lake’s clarity. It is concluded that suspended inorganic sediments and phytoplanktonic algae both contribute significantly to the reduction in clarity, and that suspended particulate matter, rather than dissolved organic matter, are the dominant causes of clarity loss.

Inle Lake is situated in the southern part of Shan State in Myanmar. It is the country’s second-largest lake, home to more than 120 000 people and a large bird sanctuary and a major source of hydroelectric power for southern Myanmar. Several distinct environmental problems have arisen in the lake basin. A long-term decrease in lake area has taken place over the last 30 years, probably because of siltation and climate. The drought of the last 2 years in particular has caused a drop in hydroelectric power output, which is affecting southern Myanmar. Many marginal parts of the lake are occupied by elephant grass mats (Saccharum spotaneum L.), known locally as kaing. These mats mature to form solid, floating islands, which are used for a unique form of agriculture but are also an increasing source of pesticide and fertilizer runoff into the lake. Textile cottage industries also abound, and both natural and manufactured dyes are discharged into the lake. Households, including many houses built on stilts in the lake, are a source of garbage and sewage. Livestock breeding also is a source of sewage. Shifting (taungyar) cultivation and village expansion has greatly increased erosion. Dredging is now necessary in many places and water clarity has decreased. The Inle carp (Cyprinus carpio intha), known locally as nga-phane, plays an important role in the food supply, as well as being a cultural symbol of the local Intha people. Nga-phane population abundance is currently low, probably because of changes in water chemistry and decreased clarity in the lake water. Partially because of the perceived potential for tourism, many sectors are now involved in lake rehabilitation and management.

Secchi depth has been measured in Lake Tahoe an average of every 12 d since July 1967. Because of the unusual clarity of the lake, Secchi depth measurement is responsive to small changes in light-attenuating particles, and the record exhibits strong variability at the seasonal, interannual, and decadal scales. Using recently developed methods of applied time-series analysis, the mechanisms of change were delineated at each scale. The seasonal pattern is a bimodal one, with two minima at approximately June and December. The June minimum is due mostly to cumulative discharge of suspended sediments following melting of the snowpack. The December minimum is probably a result of mixed-layer deepening as the thermocline passes through layers of phytoplankton and other light-attenuating particles that reach a maximum below the summer mixed layer. The interannual scale exhibits two modes of variability, one during the weakly stratified autumn‐winter period and the other during the more stratified spring‐ summer period. The first mode is a result of variable depth of mixing in this unusually deep lake, while the second results from year-to-year changes in spring runoff. A decadal trend also exists ( 20.25 m yr 21 ), resulting from accumulation of materials in the water column. It is not yet understood, however, how much of this change is due to phytoplankton or recent phytoplankton-derived materials and how much is due to other materials such as mineral suspensoids. Based on the available measurements and physical considerations, both categories may play a significant role.

The high spatial variability of estuaries poses a challenge for characterizing estuarine water quality. This problem was examined by conducting monthly high-resolution transects for several water quality variables (chlorophyll a , suspended particulate matter and salinity) in San Francisco Bay (California, U.S.A.). Using these data, six different ways of choosing station locations along a transect, in order to estimate mean conditions, were compared. In addition, 11 approaches to estimating the variance of the transect mean when stations are equally spaced were compared, and the relationship between variance of the estimated transect mean and number of stations was determined. The results provide guidelines for sampling along the axis of an estuary: (1) choose as many equally-spaced stations as practical; (2) estimate the variance of the mean y by var ( y )=(1/10 n 2 )Σ n j =2 ( y j − y j −1 ) 2 , where y 1 , . . ., y n are the measurements at the n stations; and (3) attain the desired precision by adjusting the number of stations according to var( y )α1/ n 2 . The inverse power of 2 in the last step is a consequence of the underlying spatial correlation structure in San Francisco Bay; more studies of spatial structure at other estuaries are needed to determine the generality of this relationship.

Diversion of estuarine water for human use, in conjunction with river inflow, is the main underlying cause of interannual chlorophyll variability in the landward portion of the San Francisco Bay-Delta estuary, i.e. Suisun Bay and the Sacramento-San Joaquin Delta. The principal feature of year-to-year change is high chlorophyll variability within the specific conductance range of 2–10 mS cm−1 (salinity 1–6), the approximate boundaries of an estuarine turbidity maximum (ETM). This variability stems from two separate hydrodynamic forces: (1) the strength of flow into the ETM, which affects primary productivity, losses to benthic macroinvertebrates, washout of phytoplankton cells, and chlorophyll loading; and (2) export of water from the estuary for human use, which independently affects the loading of chlorophyll from upstream sources into the ETM. In addition to the evidence for (1) presented in previous, largely descriptive studies, the simultaneous existence of both pathways is supported here by statistical models and material budgets. The source of phytoplankton organic matter from upstream was investigated further. Estimates were made for primary productivity levels in the Delta. These estimates are consistent with a mass balance for chlorophyll that suggests the Delta usually augments the flow of phytoplankton biomass from the rivers. If water were diverted from upstream of the Delta, rather than from within the Delta, the mass balance implies that both chlorophyll outflow from the Delta into the Bay, as well as primary productivity within the Delta, would increase. The primary productivity estimates also indicate that, on average, most of the phytoplankton emerging from the Delta is actually produced within the Delta, not upstream in the rivers; furthermore, most of the Delta primary productivity is respired or consumed within the Delta. A second, smaller mode of variability is as a result of phytoplankton blooms in the San Joaquin River, which were quite large and variable prior to 1978 but have been relatively small since that time. The underlying processes have not been identified in detail, but are suspected to be hydrodynamic in nature.

Background: Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. Methodology/Principal Findings: We linked a series of models to investigate responses of California’s San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010–2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. Conclusions/Significance: Most of these environmental indicators change substantially over the 21 st century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

(1990). Forest fires, atmospheric deposition and primary productivity at Lake Tahoe, California-Nevada. SIL Proceedings, 1922-2010: Vol. 24, No. 1, pp. 499-503.

The Stockton Deep Water Ship Channel, a stretch of the tidal San Joaquin River, is frequently subject to low dissolved oxygen conditions and annually violates regional water quality objectives. Underlying mechanisms are examined here using the long-term water quality data, and the efficacy of possible solutions using time-series regression models. Hypoxia is most common during June-September, immediately downstream of where the river enters the Ship Channel. At the annual scale, ammonium loading from the Regional Wastewater Control Facility has the largest identifiable effect on year-to-year variability. The longer-term upward trend in ammonium loads, which have been increasing over 10% per year, also corresponds to a longer-term downward trend in dissolved oxygen during summer. At the monthly scale, river flow, loading of wastewater ammonium and river phytoplankton, Ship Channel temperature, and Ship Channel phytoplankton are all significant in determining hypoxia. Over the recent historical range (1983–2003), wastewater ammonium and river phytoplankton have played a similar role in the monthly variability of the dissolved oxygen deficit, but river discharge has the strongest effect. Model scenarios imply that control of either river phytoplankton or wastewater ammonium load alone would be insufficient to eliminate hypoxia. Both must be strongly reduced, or reduction of one must be combined with increases in net discharge to the Ship Channel. Model scenarios imply that preventing discharge down Old River with a barrier markedly reduces hypoxia in the Ship Channel. With the Old River barrier in place, unimpaired or full natural flow at Vernalis would have led to about the same frequency of hypoxia that has occurred with actual flows since the early 1980s.

https://doi.org/10.15447/sfews.2005v3iss1art5 As in many U.S. estuaries, the tidal San Joaquin River exhibits elevated organic matter production that interferes with beneficial uses of the river, including fish spawning and migration. High phytoplankton biomass in the tidal river is consequently a focus of management strategies. An unusually long and comprehensive monitoring dataset enabled identification of the determinants of phytoplankton biomass. Phytoplankton carrying capacity may be set by nitrogen or phosphorus during extreme drought years but, in most years, growth rate is light-limited. The size of the annual phytoplankton bloom depends primarily on river discharge during late spring and early summer, which determines the cumulative light exposure in transit downstream. The biomass-discharge relationship has shifted over the years, for reasons as yet unknown. Water diversions from the tidal San Joaquin River also affect residence time during passage downstream and may have resulted in more than a doubling of peak concentration in some years. Dam construction and accompanying changes in storage-and-release patterns from upstream reservoirs have caused a long-term decrease in the frequency of large blooms since the early 1980s, but projected climate change favors a future increase. Only large decreases in nonpoint nutrient sources will limit phytoplankton biomass reliably. Growth rate and concentration could increase if nonpoint source management decreases mineral suspensoid load but does not decrease nutrient load sufficiently. Small changes in water storage and release patterns due to dam operation have a major influence on peak phytoplankton biomass, and offer a near-term approach for management of nuisance algal blooms.

[1] Shasta Lake, in northern California, has recently experienced reduced cold water storage, making it difficult to meet downstream temperature objectives for endangered winter-run chinook salmon spawning habitat. This study used a novel form of time series analysis to examine the causes, timing, and predictability of cold water storage in Shasta Lake. This analysis detected two independent modes of variability in Shasta Lake cold water storage. The first mode, representing variability during February–July and describing 64% of the overall variability in cold water storage, was negatively correlated with both the preceding year's late summer hypolimnetic discharges and that spring's air temperatures. A second mode, representing December–January and describing an additional 24% of variability, was negatively correlated with Shasta Lake fall water temperatures and winter air temperatures and positively correlated with winter inflows. These results suggest hypolimnetic discharges, air and water temperatures, and inflows act in concert to determine cold water storage in Shasta Lake. These results also suggest water column mixing should be promoted during the cold midwinter period and thermal stratification should be promoted the remainder of the year to minimize surface warming of the entire water column.

A close partnership between researchers, resources agencies, and community groups allows for the most effective ecological and economic approach to environmental protection and watershed management. One of the better documented examples of this type of cooperative effort comes from the Tahoe basin (CA-NV) where studies over the past four decades have shown that many factors including, land disturbance, habitat destruction, air pollution, soil erosion, roads, have interacted to degrade the Basin's air quality, terrestrial landscape, and streams, as well as the lake itself. For effective lake management, we need to know (1) what are the specific sources of sediment and nutrients to the lake and what are their respective contributions, (2) how much of a reduction in loading is necessary to achieve the desired lake condition (lake response), and (3) how will this reduction be achieved? In this paper we present examples of ongoing research and monitoring which are proving extremely useful in watershed management. Topics include: changes in lake clarity and the importance of long-term data; response of lake phytoplankton to nutrients and a initial budget for nitrogen and phosphorus; paleolimnological reconstruction of baseline conditions and ecosystem response to anthropogenic disturbance; a clarity model to assess lake response to management; and a sediment transport model to evaluate nonpoint source loading. Only be providing a fully integrated watershed approach can we hope to develop effective restoration/mitigation efforts so essential to providing future generations with a quality environment in the Tahoe basin. Background The role of our nation's universities in the evolving dialogue on watershed management is at a critical stage. Given the increased need to understand the (1) effects of pollution, (2) source(s), transport and fate of pollutants, and (3) continued public demand for clean air, land and water, these institutions are positioned to work closely with other stakeholders. A closer partnership between researchers, resources agencies, and community groups allows for a more effective ecological and more economic approach to environmental protection and watershed management. One of the better-documented examples of this type of cooperative effort comes from the Tahoe basin (CA-NV), where investigations by the Tahoe Research Group (TRG) at the University of California-Davis have provided clear evidence for the onset and progression of cultural eutrophication (Goldman 1988). Lake Tahoe is world-renowned for its clarity and water quality, however, continuous monitoring and research since the early 1960s has shown that algal growth is increasing at a rate greater than 5 percent per year. There has been a corresponding decline of clarity at an alarming rate of nearly one foot per year. This long-term trend in transparency is both statistically significant and is now perceivable to even the casual observer. Significant portions of the once pristine basin are urbanized. Studies by the TRG and others have shown that land disturbance, habitat destruction, air pollution, soil erosion, roads, etc. have all interacted to degrade air quality, terrestrial landscape, and streams, as well as the lake itself. We now know that once nutrients enter the lake they remain in the water, and can be recycled for decades (Jassby et al. 1995). As a consequence, the materials accumulate over time and contribute to Lake Tahoe's progressive decline. The ability of Lake Tahoe's large volume to dilute nutrient and sediment loading to levels where they have no significant affect on lake water quality has been lost.

Year-to-year fluctuations in spring mixing depth are a major source of interannual variation in primary production at Lake Tahoe, California-Nevada. The morphology of the Tahoe basin predisposes the lake to a variable spring mixing depth. The relation between mixing depth and annual production is mediated by the transport of nitrate and possibly viable biomass from below the euphotic zone.