After several weeks of very wet weather, the ground across the region was already quite saturated due to recent flooding.  This made the region susceptible to additional flooding.
An unusually strong area of low pressure for late June moved from central Pennsylvania northeastward across eastern New York during the early morning hours of Friday, June 28th.   This storm system was more typical of a winter-like storm, due to deep low pressure and heavy precipitation spiraling around the western side of the storm system.  A strong southerly flow ahead of this system transported very moist air into the region.
Heavy rainfall moved across the Mohawk Valley and western Adirondacks in advance of the low pressure during the early morning hours. The rain fell heaviest during the late night hours before tapering off during the late morning.  Rainfall fell at rates of nearly one inch per hour at times with three to five inches of rainfall having occurred in total. This led to significant flash flooding across both the Mohawk Valley and Adirondacks.
Many roads were washed out and closed, including a portion of the New York State Thruway between exits 29 (Canajoharie) and 29A (Little Falls).  In addition, urbanized areas along the Mohawk River experienced dangerous amounts of flooding.  The entire town of Fort Plain was under water and many swift water rescues had to take place.  Many homes and trailers were impacted by flood waters.  The New York State Barge Canal was closed as a result of the flooding.  In addition, one fatality occurred as a result of the flooding.
State of emergencies were declared in many communities as a result of the flooding including:  Herkimer County, Montgomery County, Village of Ilion (Herkimer County),  Town and Village of Herkimer (Herkimer County), Village of Mohawk (Herkimer County), Town of Johnsburg (Warren County), Town of Minden (Montgomery County), and the Town of German Flatts (Herkimer County).

On July 12th, President Obama signed a New York Disaster Declaration and ordered federal aid to supplement state and local recovery efforts in the area affected by severe storms and flooding during the period of June 28 to July 4, 2013. This included Herkimer, Montgomery and Warren counties in east central New York.

Flash Flood in MONTGOMERY, NEW YORK
From 28-JUN-13 05:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: CANAJOHARIE
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: 911 Call Center

Significant flooding occurred throughout Canajoharie due to flash flooding from heavy rainfall, especially for areas along the Canajoharie Creek.  Interstate 90 (The New York State Thruway) was closed between exits 29 and 29A due to flooding.

Flash Flood in WARREN, NEW YORK
From 28-JUN-13 07:30:00 to 28-JUN-13 12:00:00 (EST-5)
Location: BAKERS MILLS
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Broadcast Media

Flash flooding occurred in the Bakers Mills section of Johnsburg due to heavy rainfall.  Water rescue teams were deployed to several homes that were threatened by flooding.  A state of emergency was declared for the town as a result of the flooding.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 04:23:00 to 28-JUN-13 11:30:00 (EST-5)
Location: EATONVILLE
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: River/Stream Gage

The river gage at Kast Bridge recorded flash flooding as a result of heavy rainfall.   The river gage crested at 9.01 feet at 6:15 AM EST, which was the second highest crest on record.  The river gage at Kast Bridge is located along on the right bank of the West Canada Creek 600 feet downstream from a bridge on old State Highway 28 at Kast Bridge, 1.2 miles downstream from North Creek, 2.2 miles north of Herkimer, and 4.0 miles upstream from the river's mouth at the Mohawk River.

Flood in HERKIMER, NEW YORK
From 28-JUN-13 11:30:00 to 28-JUN-13 18:02:00 (EST-5)
Location: LITTLE FALLS
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: River/Stream Gage

Flooding due to heavy rainfall earlier in the day continued along the Mohawk River at the Little Falls gage. The gage slowly fell during the day until dropping below flood stage in the evening hours at 6:02 PM EST.  The Little Falls gage is located on left bank of the river, 1,800 ft downstream from Fivemile Dam, 2.0 miles upstream from East Canada Creek, and 4.5 miles southeast of city of Little Falls.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 03:30:00 to 28-JUN-13 11:30:00 (EST-5)
Location: EAST FRANKFORT
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Fire Department/Rescue

Flash flooding occurred throughout Ilion due to heavy rainfall. Water rescues and evacuations had to take place. Some roads were washed out and damaged due to the flooding.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 03:45:00 to 28-JUN-13 11:30:00 (EST-5)
Location: EAST HERKIMER
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Fire Department/Rescue

Numerous roads were washed out and closed as a result of flash flooding in the city of Herkimer.  Some residences were impacted by flood waters.  A state of emergency was declared for the city of Herkimer.  Some water rescues and evacuations took place as well.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 03:45:00 to 28-JUN-13 11:30:00 (EST-5)
Location: EATONVILLE
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Fire Department/Rescue

Numerous roads were washed out in the southwestern side of the town of Fairfield due to flash flooding from heavy rainfall.  Some water rescues and evacuations took place.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 04:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: INDIAN CASTLE
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Department of Highways

New York State Route 5S near Interstate 90 was closed in Indian Castle due to flash flooding from heavy rainfall.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 04:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: MOHAWK
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: State Official

Flash flooding occurred throughout the town of German Flatts due to heavy rainfall.  A trailer park was evacuated due to the flooding.  A state of emergency was declared for the entire town.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 04:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: EAST SCHUYLER
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: 911 Call Center

Roads were closed throughout Frankfort due to flash flooding from heavy rainfall.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 04:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: MIDDLEVILLE
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: 911 Call Center

Route 28 was closed in the town of Middleville due to flash flooding from heavy rainfall.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 04:15:00 to 28-JUN-13 11:30:00 (EST-5)
Location: EAST SCHUYLER
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: 911 Call Center

New York State Route 5 was closed between Millers Grove Road and Watkins Road due to flash flooding from heavy rainfall.

Flash Flood in MONTGOMERY, NEW YORK
From 28-JUN-13 05:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: FT PLAIN
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Broadcast Media

Flash flooding occurred throughout Fort Plain due to heavy rainfall.  Fifty to one hundred people were trapped in homes and water rescues needed to take place.  Media reported up to two hundred homes were damaged or destroyed by flooding.  Every road within the town was under water and some bridges were damaged or destroyed.  One fatality occurred as flood waters swept a woman from a trailer away.

Flash Flood in MONTGOMERY, NEW YORK
From 28-JUN-13 05:00:00 to 28-JUN-13 11:30:00 (EST-5)
Location: ST JOHNSVILLE
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: 911 Call Center

Significant flash flooding occurred throughout St. Johnsville due to heavy rainfall.  Several homes were affected by flood waters.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 05:21:00 to 28-JUN-13 11:30:00 (EST-5)
Location: LITTLE FALLS
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: River/Stream Gage

Flash flooding occurred along the Mohawk River at the Little Falls River Gage.  The gage crested at 18.22 feet at 9:00 AM EST, which is considering major flooding and is the sixth highest crest on record. The Little Falls gage is located on left bank of the river, 1,800 feet downstream from Fivemile Dam, 2.0 miles upstream from East Canada Creek, and 4.5 miles southeast of city of Little Falls.

Flash Flood in HERKIMER, NEW YORK
From 28-JUN-13 03:30:00 to 28-JUN-13 11:30:00 (EST-5)
Location: ILION
Flood cause: Heavy Rain
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Fire Department/Rescue

Numerous roads were closed in Mohawk due to flash flooding from heavy rainfall.  Water rescues and evacuations took place across the entire town.  The hardest hit areas were along the Fulmer Creek.