Long term drought impacts continued through the month of September, although some of the largest of the reservoirs in northern interior California continued to be around normal levels. While there was a better snow pack for the mountains over the wet season, very warm weather caused the snow to melt and run off quickly in the spring. This caused peak reservoir levels to occur earlier than expected. At the end of September, all but Lake Shasta and Don Pedro were dropping off faster than normal. Lake Shasta was 105% of normal by the end of the month, Lake Oroville was 75%, Folsom Lake was 56%, and Don Pedro was 96%. New Melones continued to lag behind the other significant area reservoirs and was only 39% of normal.
The U.S. Drought Monitor showed no change from August for the area, with severe drought across the southern Sacramento Valley; the northern and central Sacramento Valley and the northern Sierra in moderate drought, while Shasta County was abnormally dry. The remainder of the Central and northern portion of the Southern Sierra Nevada mountain areas remained in the severe to extreme drought. There remained extreme drought in the Sierra south of Highway 50.
Groundwater aquifers continued to recharge much more slowly than the surface reservoirs, with many in the Central Valley still falling toward record levels. Growers in the San Joaquin Valley continued to turn to groundwater with reduced surface water allocations. This heavy reliance on groundwater resulted in declining water levels.
Governor Jerry Brown declared a drought emergency for the entire state of California January 17, 2014 and this continued to be in effect. Governor Brown issued an executive order on May 9, 2016 that built on temporary statewide emergency water restrictions to establish longer-term water conservation measures, including permanent monthly water use reporting, new permanent water use standards in California communities and banned clearly wasteful practices such as hosing off sidewalks, driveways and other hardscapes.
Local Emergency proclamations remain for Colusa, Calaveras, El Dorado, Glenn, Plumas, San Joaquin, Shasta, Stanislaus, Sutter, Tuolumne, and Yuba counties. The cities of Live Oak (Sutter County), Lodi (San Joaquin County), Manteca (San Joaquin County), Portola (Plumas County), Ripon (San Joaquin County), and West Sacramento (Yolo County). Drought task forces remain in Lake, Nevada, Placer, Plumas, Sacramento, San Joaquin, Stanislaus, Sutter, Tehama, Tuolumne, and Yolo counties to coordinate response to the drought.
Mandatory water reductions of 25% as ordered by Governor Brown were suspended in May due to the improved reservoir levels, with voluntary reductions requested.
The state continued to supply food assistance to those impacted by the drought, along with California Disaster Assistance Act money for those who have lost drinking water due to dry wells. Nonprofit organizations in the San Joaquin Valley struggled to meet the needs of their clients for drought-related programs.
Tree mortality from drought and resulting bark beetle infestation continued to increase both in scale and intensity, especially in low elevation pine and oak woodlands along the Sierra Nevada Range. A US Forest Service- Forest Health Protection aerial survey showed tree mortality was especially high in the Stanislaus National Forest southward, though pockets of tree mortality were present as far north as eastern Shasta County. Tree mortality from the recent years of drought has been estimated at 66 million trees across California. This increase in dead and dying trees made the forest more susceptible to wildfires.
Drought conditions are blamed for an increase in blue-green algae across Northern California lakes, with a concentration of these in Shasta County. These algae can produce cyanotoxins, which in high enough concentrations can potentially cause allergic reactions, skin irritation, fever, diarrhea, vomiting, joint pain, liver damage and even cancer in people and pets swimming in the water.

Drought in MOTHERLODE/CAMPTONVILLE TO GROVELAND, CALIFORNIA
From 01-SEP-16 00:00:00 to 19-SEP-16 23:59:00 (PST-8)
Property damage: 0.00K
Crop damage: 0.00K
Reported by: State Official

The Household Water Supply Shortage Reporting System indicated there were some homes without well water due to dry wells. Calaveras County had 1 household and Tuolumne County had 240 households, unchanged from August.

Drought in NORTHERN SAN JOAQUIN VALLEY, CALIFORNIA
From 01-SEP-16 00:00:00 to 19-SEP-16 23:59:00 (PST-8)
Property damage: 0.00K
Crop damage: 0.00K
Reported by: State Official

The Household Water Supply Shortage Reporting System indicated there were some homes without well water due to dry wells. There were 228 in Stanislaus County and 11 in San Joaquin County, unchanged since August. Many communities in the Northern San Joaquin Valley were still receiving food assistance as a direct result of the drought.