Long term drought impacts continued through the month of June, though the largest of the reservoirs in northern interior California were at or near normal levels due to a significant mountain snow pack melting. Very warm weather caused the snow to melt and run off earlier than expected, though.  The California Department of Water Resources revised its water supply estimate downward and predicted just 71% of the normal runoff during the months of heaviest snowmelt, reducing the water rivers and reservoirs usually receive. Lake Shasta was 107% of normal by the end of the month, Lake Oroville was 102%, Folsom Lake was 88%, and Don Pedro was 97%. New Melones continued to lag behind the other significant area reservoirs and was only 41% of normal. On April 21st, the Department of Water Resources increased water delivery projections to the State Water Project to 60%, up from the 45% estimate in late March.
The U.S. Drought Monitor showed no change from May 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 recharged much more slowly than the surface reservoirs, with many in the Central Valley still falling toward record levels. Growers in the San Joaquin Valley continue to turn to groundwater with reduced surface water allocations. This heavy reliance on groundwater has 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.
The local Emergency Proclamation for Butte County was removed in June. 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 Water Board announced on June 6th that water conservation was strong in April with residents statewide reducing water use by 26.1% over the same month in 2013. In contrast, water conservation fell to 21.5% savings for the month of June 2016, down from 27.5% in June 2015.
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.
Drought conditions are blamed for an increase in blue-green algae across Northern California lakes. 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.

Drought in NORTHERN SAN JOAQUIN VALLEY, CALIFORNIA
From 01-JUN-16 00:00:00 to 30-JUN-16 23:59:00 (PST-8)
Reported by: State Official

The Household Water Supply Shortage Reporting System indicated there were some homes without well water due to dry wells, with 228 in Stanislaus County and 10 in San Joaquin County, both unchanged since May. However, many communities in the Northern San Joaquin valley were still receiving food assistance as a direct result of the drought.

Drought in MOTHERLODE/CAMPTONVILLE TO GROVELAND, CALIFORNIA
From 01-JUN-16 00:00:00 to 30-JUN-16 23:59:00 (PST-8)
Reported by: State Official

The Household Water Supply Shortage Reporting System had Calaveras County with 1 household, Tuolumne County had 238 households, unchanged from May.

Drought in NORTHERN SACRAMENTO VALLEY, CALIFORNIA
From 01-JUN-16 00:00:00 to 30-JUN-16 23:59:00 (PST-8)
Reported by: State Official

The Household Water Supply Shortage Reporting System indicated there were still some homes without well water due to dry wells, with 3 in Shasta County, unchanged from May. Tehama County was 34, also unchanged from May.

Drought in CENTRAL SACRAMENTO VALLEY, CALIFORNIA
From 01-JUN-16 00:00:00 to 30-JUN-16 23:59:00 (PST-8)
Reported by: State Official

The Household Water Supply Shortage Reporting System indicated there were some homes without well water due to dry wells with 25 in Glenn County, unchanged from May. Colusa County had 4, also unchanged. Butte County had 1 dry well, up from 0 wells in May.

Drought in SOUTHERN SACRAMENTO VALLEY, CALIFORNIA
From 01-JUN-16 00:00:00 to 30-JUN-16 23:59:00 (PST-8)
Reported by: State Official

The Household Water Supply Shortage Reporting System indicated there were some homes without well water due to dry wells, with 1 in Yolo County and 1 in Sacramento County, unchanged from May.

Drought in CARQUINEZ STRAIT AND DELTA, CALIFORNIA
From 01-JUN-16 00:00:00 to 30-JUN-16 23:59:00 (PST-8)
Reported by: State Official

The Household Water Supply Shortage Reporting System had 1 home without well water in Solano County, unchanged from May.