With a reputation as a somewhat uninspiring but methodical politician, Spidla set out to lead his 101-seat coalition composed of the Social Democrats, Christian Democrats, and Freedom Union in the direction of EU membership. Following the June 2002 elections, Spidla named 16 other members of the cabinet and claimed the government would be a strong one.
Spidla was faced with his first crucial test as prime minister in August 2002, when the Czech Republic was hit with torrential rains that caused the most catastrophic flooding in the country's modern history. The floods culminated in Prague on 14 August, when the water in the Vltava River reached its peak. The floods began to subside on 17 August, but they affected 10 regions and 753 municipalities. About 220,000 people were evacuated and 17 people were killed as a result of the flooding. Over 1,000 homes were destroyed, and the Prague metro was particularly hard hit, with half of its stations ceasing operations due to flooding and damage. Spidla later reacted in a televised speech by stating the country would cope with the floods, and that it had enough strength to help affected citizens and undertake reconstruction.
In early 2003, Spidla faced opposition from within his own party in the elections for president held in February. Vaclav Klaus, Spidla's long-time opponent, was elected president on 28 February, after several members of the CSSD voted for Klaus instead of the party's own candidate. Klaus's victory prompted Spidla to call a vote of confidence in Parliament on 11 March. Spidla's calling of the confidence vote was seen as an assertion of authority over his own party as much as the election of Klaus itself. A sizeable faction of Spidla's CSSD is loyal to Spidla's predecessor, Milos Zeman, and does not approve of the coalition formed with the center-right Christian Democrats and Freedom Union. Spidla does not favor forming a coalition with the Communists or Klaus's Civic Democrats, as do some of the opposition members of his party. Spidla reshuffled his cabinet and indicated he would wait until the Social Democrats would hold their annual conference to see if he would be reelected as party leader.