By September, the Confederates still occupied the Commonwealth over much of the Bluegrass. The Confederate Army under General Bragg invaded from Tennessee and attacked a much smaller force of U.S. troops under Colonel Wilder defending Munfordville in Hart County. On 16 September, Colonel Wilder under a truce was given an escorted tour of the much superior Confederate Army. After negotiations, the three U.S. Regiments surrendered on 17 September 1862 giving the Confederates control of the railroad bridge. The drought had allowed rapid movement of a large Confederate army over dry roads.

The summer drought had not relented and water supplies were failing. Spring branches stopped flowing and many farm ponds dried up. The Battle of Munfordville began with an attack by the Confederate force about dawn on Sunday, 14 September 1862. At about that same time in Louisville at the corner of Second and Chestnut, Druggist E. N. Woodruff was taking the morning climate observations for the Smithsonian Institution. He recorded a warm 62°F at 7 a.m., the relative humidity was 88%, the sky was clear, very light surface winds were from the north, and the barometer measured 29.81 inches. After the morning battle, a truce was called while the dead were buried and the wounded were removed to hospitals. At two p.m. the temperature in Louisville in Jefferson County was 88°F and the relative humidity was 50%. The work under the truce continued through the night and into Monday morning (15 September 1862). At 7 a.m. that morning, Mr. Woodruff entered the temperature as 70°F with a relative humidity of 90%. The sky was still clear and the surface wind was from the west. The pressure was steady at 29.82 inches. By 2 p.m., the temperature reached 83°F as scattered cirrocumulus clouds appeared from the southwest. On 16 September, during Colonel Wilder's escorted inspection. Temperature rose from 70°F at 7 a.m. to 86°F at 2 p.m. as clouds covered nine-tenths of the sky. Relative humidity fell to 58% and winds shifted to come from the northwest. By 9 p.m. that evening, the temperature cooled to 74°F. By the next morning (17 September 1862), it had cooled only to 71°F with a relative humidity of 85%. The falling barometer read 29.63 inches. The battle was over but the rather hot September day was not.