Populations of native and introduced aquatic organisms in the San Fran
cisco Bay/Sacramento-San Joaquin Delta Estuary (''Bay/Delta'') have un
dergone significant declines over the past two decades. Decreased rive
r inflow due to drought and increased freshwater diversion have contri
buted to the decline of at least some populations. Effective managemen
t of the estuary's biological resources requires a sensitive indicator
of the response to freshwater inflow that has ecological significance
, can be measured accurately and easily, and could be used as a ''poli
cy'' variable to set standards for managing freshwater inflow. Positio
ning of the 2 parts per thousand (grams of salt per kilogram of seawat
er) bottom salinity value along the axis of the estuary was examined f
or this purpose. The 2 parts per thousand bottom salinity position (de
noted by X(2)) has simple and significant statistical relationships wi
th annual measures of many estuarine resources, including the supply o
f phytoplankton and phytoplankton-derived detritus from local producti
on and river loading; benthic macroinvertebrates (molluscs); mysids an
d shrimp; larval fish survival; and the abundance of planktivorous, pi
scivorous, and bottom-foraging fish. The actual mechanisms are underst
ood for only a few of these populations. X(2) also satisfies other rec
ognized requirements for a habitat indicator and probably can be measu
red with greater accuracy and precision than alternative habitat indic
ators such as net freshwater inflow into the estuary. The 2 parts per
thousand value may not have special ecological significance for other
estuaries (in the Bay/Delta, it marks the locations of an estuarine tu
rbidity maximum and peaks in the abundance of several estuarine organi
sms), but the concept of using near-bottom isohaline position as a hab
itat indicator should be widely applicable. Although X(2) is a sensiti
ve index of the estuarine community's response to net freshwater inflo
w, other hydraulic features of the estuary also determine population a
bundances and resource levels. In particular, diversion of water for e
xport from or consumption within the estuary can have a direct effect
on population abundance independent of its effect on X(2). The need to
consider diversion, in addition to X(2), for managing certain estuari
ne resources is illustrated using striped bass survival as an example.
The striped bass survival data were also used to illustrate a related
important point: incorporating additional explanatory variables may d
ecrease the prediction error for a population or process, but it can i
ncrease the uncertainty in parameter estimates and management strategi
es based on these estimates. Even in cases where the uncertainty is cu
rrently too large to guide management decisions, an uncertainty analys
is can identify the most practical direction for future data acquisiti
on.