The storm dropped heavy rainfall along its path, peaking at over 40 inches (1,000 mm) in Texas. The worst flooding occurred in Houston, where most of Allison's damage occurred: 30,000 became homeless after the storm flooded over 70,000 houses and destroyed 2,744 homes. Downtown Houston was inundated with flooding, causing severe damage to hospitals and businesses. Twenty-three people died in Texas. Throughout its entire path, Allison caused $6.7 billion (2008 USD) in damage and 41 deaths. Aside from Texas, the places worst hit were Louisiana and southeastern Pennsylvania.
Following the storm, President George W. Bush designated 75 counties along Allison's path as disaster areas (the first time he had to do so), which enabled the citizens affected to apply for aid. Allison is the only tropical storm to have its name retired without ever having reached hurricane strength.
Allison initially had subtropical characteristics with an upper level low to the southwest of the circulation. Despite this, the storm quickly strengthened to a 60 mph (95 km/h) storm, though tropical storm force winds extended up to 230 miles (370 km) east of the center. Allison weakened while nearing the Texas coastline, and struck near Freeport, Texas as a 50 mph (80 km/h) tropical storm late on June 5. The storm quickly weakened over land, and the National Hurricane Center discontinued advisories early on June 6. The depression drifted northward until reaching Lufkin, Texas, where it stalled due to a high pressure system to its north. On June 8, the depression drifted to the south, then to the southwest. Early on June 10, Allison again reached the Gulf of Mexico just 22 miles (35 km) west of its original landfall location. Due to dry air and moderate westerly wind shear, the storm transformed into a subtropical cyclone. While the subtropical depression moved eastward, a new low level circulation redeveloped to the east, and Allison quickly made landfall on Morgan City, Louisiana on June 11. Strong thunderstorms redeveloped over the circulation, and Allison strengthened into a subtropical storm over southeastern Louisiana.
Allison re-strengthened to reach winds of 45 mph (72 km/h), and an eyewall feature briefly existed. The feature was transient, and Allison quickly weakened back to a tropical depression. The depression tracked to the east-northeast through Mississippi, Alabama, Georgia, and South Carolina before becoming nearly stationary near Wilmington, North Carolina. It drifted through the state, and accelerated to the northeast in response to an approaching cold front. Allison reached the Atlantic Ocean on June 17, and briefly reintensified to a subtropical storm through baroclinic processes. Allison became extratropical while south of Long Island on June 18, and was absorbed by the cold front on the next day.
In Tallahassee, Florida, a shelter opened the day prior to Allison's movement northward through the area, seven staff members housing 12 people. Two other shelters were on standby. Teams informed citizens in the Florida Panhandle of flood dangers.
Houston experienced torrential rainfall in a short amount of time. The six-day rainfall in Houston amounted to 38.6 inches (980 mm). Two-thirds of the bayous and creeks in Harris County experienced 500-year flood events. The deluge of rainfall flooded 95,000 automobiles and 73,000 houses throughout Harris County. Tropical Storm Allison destroyed 2,744 homes, leaving 30,000 homeless with residential damages totaling to $1.76 billion (2001 USD, $2.05 billion 2007 USD).
Several hospitals in the Texas Medical Center, the largest medical complex in the world, experienced severe damage from the storm, which hit quickly and with unexpected fury on a Friday evening. The Baylor College of Medicine experienced major damage, totaling $495 million (2001 USD, $577 million 2007 USD). The medical school lost 90,000 research animals, 60,000 tumor samples, and 25 years of research data. The University of Texas Health Science Center at Houston, across the street, lost thousands of laboratory animals. Throughout the Medical Center, damage totaled to over $2 billion (2001 USD, $2.3 billion 2007 USD).
The underground tunnel system, which connects most large office buildings in downtown Houston, was submerged, as were many streets and parking garages adjacent to Buffalo Bayou. At the Theatre District, also in downtown, the Houston Symphony, Houston Grand Opera, and Alley Theater lost millions of dollars of costumes, musical instruments, sheet music, archives and other artifacts. By midnight on June 9 nearly every freeway and major road in the city was under several feet of water, forcing hundreds of motorists to abandon their vehicles for higher ground.
Despite massive flooding damage to entire neighborhoods there were no drowning deaths in flooded homes. In the area, there were 12 deaths from driving, 6 from walking, 3 from electrocution, and 1 in an elevator. Elsewhere in Texas, a man drowned when swimming in a ditch in Mauriceville. Damage totaled to $5.2 billion (2001 USD, $6 billion 2007 USD) throughout Texas.
While making its first landfall, Allison's large circulation dropped severe rains on southwest Louisiana. Days later, Allison hit the state as a subtropical storm, dropping more heavy rains to the area. Rainfall totals peaked at 29.86 inches (758 mm) in Thibodaux, the highest rainfall total in Louisiana from a tropical cyclone since a previous Tropical Storm Allison in 1989. Most of the southeastern portion of the state experienced over 10 inches of rain (255 mm). Winds were generally light, peaking at 38 mph (61 km/h) sustained in Lakefront with gusts to 53 mph (85 km/h) in Bay Gardene. The storm produced a storm surge of 2.5 feet (0.75 m) in Cameron as it was making landfall in Texas. While moving northward through Texas, the outer bands of the storm produced an F1 tornado near Zachary, damaging several trees and a power line. A man was killed when a damaged power line hit his truck.
When Allison first made landfall, heavy rainfall flooded numerous houses and businesses. Minor wind gusts caused minor roof damage to 10 houses in Cameron Parish, while its storm surge flooded portions of Louisiana Highway 82. When the system returned, more rainfall occurred, flooding over 1,000 houses in St. Tammany Parish, 80 houses in Saint Bernard Parish, and hundreds of houses elsewhere in the state. The flooding also forced 1,800 residents from their homes in East Baton Rouge Parish. The deluge left numerous roads impassable, while runoff resulted in severe river flooding. The Bogue Falaya River in Covington crested past its peak twice to near record levels. The Amite and Comite Rivers reached their highest levels since 1983. In addition, the levee along the Bayou Manchac broke, flooding roadways and more houses. Damage in Louisiana totaled to $65 million (2001 USD, $75 million 2007 USD).
In Mississippi, Allison produced heavy rainfall of over 10 inches (255 mm) in one night, while some areas in the southwestern portion of the state received over 15 inches (380 mm). The flooding damaged numerous houses and flooded many roadways. Thunderstorms from the storm produced four tornadoes, including one in Gulfport, Mississippi that damaged 10 houses. Severe thunderstorms in George County damaged 15 houses, destroyed 10, and injured five people. Damage in Mississippi totaled to over $1 million (2001 USD, $1.2 million 2007 USD). Rainfall in Alabama was moderate, with areas near Mobile experiencing more than 10 inches (255 mm). Heavy rainfall closed several roads in Crenshaw County. The storm, combined with a high pressure, produced coastal flooding in southern Alabama. Allison produced an F0 tornado in southwest Mobile County that caused minor roof damage and another F0 tornado in Covington County that caused minor damage to six homes and a church.
The storm, combined with a high pressure system, produced a strong pressure gradient, resulting in strong rip currents off the coast of Florida. The currents prompted sirens, which are normally used for storm warnings, to be activated in Pensacola Beach. The rip currents killed 5 off the coast of Florida. Outer rain bands from the storm dropped heavy rainfall across the Florida Panhandle of over 11 inches (280 mm) in one day. The Tallahassee Regional Airport recorded 10.13 inches (257 mm) in 24 hours, breaking the old 24 hour record set in 1969. Throughout the state, Allison destroyed 10 homes and damaged 599, 196 severely, primarily in Leon County. Including the deaths from rip currents, Allison killed eight people in Florida and caused $20 million (2001 USD, $23 million 2007 USD) in damage.
Over Georgia, the storm dropped heavy rainfall of 10 inches (255 mm) in 24 hours in locations. The deluge caused rivers to crest past their banks, including the Oconee River at Milledgeville which peaked at 33.7 feet (10.3 m). The rainfall, which was heaviest across the southwestern portion of the state, washed out several bridges and roads, and flooded many other roads. Georgia governor Roy Barnes declared a state of emergency for seven counties in the state. The storm also spawned two tornadoes. In South Carolina, Allison's outer bands produced 10 tornadoes and several funnel clouds, though most only caused minor damage limited to a damaged courthouse, snapped trees and downed power lines. Allison produced from 12 to 16 inches (305 to 406 mm) of rainfall in North Carolina, closing nearly all roads in Martin County and damaging 25 homes. The severe flooding washed out a bridge in eastern Halifax County and flooded numerous cars. Wet roads caused nine traffic accidents throughout the state.
In Virginia, Allison produced light rainfall, with the southeastern and south-central portions of the state experiencing over 3 inches (76 mm). A tree in a saturated ground fell over and killed one person. Allison also produced one tornado in the state. Washington, D.C. experienced moderate rainfall from the storm, totaling to 2.59 inches (66 mm) in Georgetown. In Maryland, rainfall from Tropical Depression Allison totaled to 7.5 inches (190 mm) in Denton, closing eleven roads and causing washouts on 41 others. The Maryland Eastern Shore experienced only minor rainfall from one to two inches (25 to 50 mm). Damage was light, and no deaths were reported. In Delaware, the storm produced moderate rainfall, peaking at 4.2 inches (106 mm) in Greenwood. No damage was reported.
Allison, in combination with an approaching frontal boundary, dropped heavy rainfall across southeastern Pennsylvania, peaking at 10.17 inches (258 mm) in Chalfont in Bucks County and over 3 inches (76 mm) in portions of Philadelphia. The rainfall caused rivers to rise, with the Neshaminy Creek in Langhorne peaking at . Several other rivers and creeks in southeastern Pennsylvania crested at over 10 feet (3 m). The rainfall downed numerous weak trees and power lines, leaving 70,000 without power during the storm. The flooding washed out several roads and bridges, including a few SEPTA rail lines. In addition, the rainfall destroyed 241 homes and damaged 1,386 others. Flooding at a Dodge dealership totaled 150 vehicles. Hundreds of people were forced to be rescued from damaged buildings from flood waters. The flooding dislodged a clothes dryer in the basement of the "A" building of the Village Green Apartment Complex in Upper Moreland Township, breaking a natural gas line. The gas leak resulted in an explosion and an ensuing fire that killed six people. Firefighters were unable to render assistance as the building was completely surrounded by floodwaters. Additionally, one man drowned in his vehicle in a river. Damage in Pennsylvania totaled to $215 million (2001 USD, $250 million 2007 USD).
In New Jersey, the storm produced heavy rainfall, peaking at 8.1 inches (205 mm) in Tuckerton. The rains also caused river flooding, including the north branch of the Metedeconk River in Lakewood which crested at 8 feet (2.5 m). The flooding, severe at places, closed several roads, including numerous state highways. Gusty winds of up to 44 mph (71 km/h) in Atlantic City downed weak trees and power lines, leaving over 13,000 without power. Several people had to be rescued from high waters, though no fatalities occurred in the state. Overall damage was minimal.
Tropical Storm Allison caused flash flooding in New York, dropping up to 3 inches (75 mm) of rain in one hour in several locations and peaking at 5.73 inches (146 mm) in Granite Springs. The rains also caused river flooding, including the Mahwah River which crested at . Allison's rainfall damaged 24 houses and several stores, while the flooding closed several major highways in the New York City area. Overall damage was light, and no fatalities occurred in New York due to Allison. Similarly, rainfall in Connecticut peaked at 7.2 inches (183 mm) in Pomfret, closing several roads and causing minor damage to numerous houses. The Yantic River at Yantic crested at 11.1 feet (3.4 m), while a state road was closed when a private dam in Hampton failed from the rainfall. In Rhode Island, Allison produced up to 7.1 inches (180 mm) of rainfall in North Smithfield, washing out several roads and houses, and destroying a log house in Foster.
An isolated severe thunderstorm in the outer bands of Allison produced an F1 tornado in Worcester and Middlesex Counties in Massachusetts, impacting over 100 trees and damaging one house and one small camper. A microburst in Leominster and another in Shirley damaged several trees. Lightning from the storm hit two houses, causing significant damage there but little elsewhere. Allison also produced moderate rainfall in the state, mainly ranging from 3 to 5 inches (75 to 125 mm). The rainfall caused drainage and traffic problems. Damage in Massachusetts totaled to $400,000 (2001 USD, $466,000 2007 USD).
A few weeks after Allison, FEMA opened six disaster recovery centers across southeast Texas, which provided recovery information to those who applied for disaster assistance. The American Red Cross and the Salvation Army opened 48 shelters at the peak of need for people driven from their homes, which served nearly 300,000 meals. The National Disaster Medical System deployed a temporary hospital to Houston with 88 professionals, aiding nearly 500 people. Thirty-five volunteer services provided aid for the flood victims in Texas, including food, clothing, and volunteers to help repair the houses. After nearly 50,000 cars were flooded and ruined, many people attempted to sell the cars across the country without telling of the car's history. Following the extreme flooding, a mosquito outbreak occurred, though FEMA provided aid to control the problem. By six months after the storm, around 120,000 Texas citizens applied for federal disaster aid, totaling to $1.05 billion (2001 USD, $1.22 billion 2007 USD).
Like in Texas, a mosquito outbreak occurred in Louisiana. Only pesticides acceptable to the US Environmental Protection Agency and the US Fish and Wildlife Service were allowed to be used. FEMA officials warned homeowners of the dangers of floodwaters, including mold, mildew, and bacteria. By three months after the storm, just under 100,000 Louisiana citizens applied for federal aid, totaling to over $110 million (2001 USD, $128 million 2007 USD). $25 million (2001 USD, $29 million 2007 USD) of the total was for business loans, while an additional $8 million was for public assistance for communities and state agencies. More than 750 flood victims in Florida applied for governmental aid, totaling to $1.29 million (2001 USD, $1.5 million 2007 USD). In Pennsylvania, 1,670 flood victims applied for federal aid, totaling to $11.5 million (2001 USD, $13.4 million 2007 USD). $3.4 million (2001 USD, $4 million 2007 USD) of the total was to replace a SEPTA rail bridge over the Sandy Run Creek in Fort Washington.