Due to the cyclone’s slow movement over Louisiana, it dropped over 10 in (250 mm) of rainfall across much of the southern portion of the state. The intense rainfall increased levels along rivers in southwestern Louisiana. High waves and a storm surge of 5 to 8 ft (1.5 to 2.4 m) flooded low-lying and coastal areas of southeastern Louisiana. The hurricane’s erratic path prevented farmers from harvesting crops for three days. The combination of flooding from rainfall and storm surge covered widespread areas of crop fields, mostly affecting soybean and sugar. Other crops in the state had previously been harvested. About 200 cattle drowned in Terrebonne Parish, and thousands were stranded. Crop damage was estimated at over $304 million, including $100 million to the soybean industry, and with statewide damage estimated at $1 billion. In addition to the crop damage, Juan severely affected the shrimp industry by washing many shrimp offshore and killing others. The storm left about $2.9 million in damage to oil facilities in the state, including the costs for damaged pipelines. Overall, Juan flooded about 50,000 houses in Louisiana, causing $250 million in property damage.
Near Port Fourchon in Lafourche Parish, the storm surge damaged portions of Louisiana Highways 1 and 3090 and flooded about 1,200 homes, some to their roofs. Two levees in the parish were washed out and one was overflown, flooding 100 houses near Lockport. In Terrebonne Parish, the powerful storm surge swept away parked cars, knocked a home off its foundation, and damaged a 300 ft (91 m) portion of a levee. In the parish, 800 homes were flooded, and 15,000 people were left homeless. The storm surge also washed out a 6,000 ft (1,800 m) portion of the levee protecting Grand Isle, and damaged another 14,000 ft (4,300 m). The levee, built in 1984, sustained $500,000 in damages, which flooded the island with 4 ft (1.2 m) of ocean water. Most of the island lost power, and the city hall and high school, set up as shelters, utilized generators during the storm. In Jefferson Parish, which contains Grand Isle, the storm surge entered 2,233 homes and inundated about 3,100 cars. In Violet, a man drowned he fell from his boat into a flooded canal, and another fisherman drowned in Atchafalaya Bay. The surge flooded a 3 mi (4.8 km) section of Louisiana Route 23 in Plaquemines Parish, entering several homes, as well as a portion of Route 22. Between Livingston and Ascension parishes, about 800 homes were flooded, and another 53 homes were flooded in Tangipahoa Parish. Waters from Lake Pontchartrain swept over Airline Highway and portions of a 4 ft (1.2 m) high levee, flooding 250 nearby homes. The storm surge washed out three bridges and flooded 800 homes in St. Tammany Paris, while high waters killed a man in Slidell. One man was electrocuted and killed in Arnaudville when stepping on a downed wire.
While approaching its final landfall as a weak tropical storm, Juan created a storm surge of 6.5 ft (2.0 m) along the Chandeleur Islands to its west, resulting in extensive beach erosion. The island chain is an important buffer to parts of mainland Louisiana against storms, but is frequently physically manipulated by intense hurricanes. Hurricanes Danny and Elena also impacted the islands in 1985. Large portions of the Louisiana coastline lost 40 to 100 ft (12 to 30 m) of beaches due to the storm, with several new temporary inlets created along barrier islands.