Clubroot, a disease of Brassicaceae species, is caused by the soilborne pathogen Plasmodiophora brassicae. High soil water content was previously described to favour the motility of zoospores and their penetration into root cells. In this study, the effect of irrigation regimes on clubroot development during the post-invasive secondary phase of infection was investigated. Three irrigation regimes (low, standard, high) were tested on two Arabidopsis accessions, Col-0 (susceptible) and Bur-0, a partially resistant line. In Col-0, clubroot symptoms and resting spore content were higher under the ‘low irrigation’ regime than the other two regimes, thus enhancing the phenotypic contrast between the two Arabidopsis accessions. Clubroot severity under high and low irrigation regimes was evaluated in near-isogenic lines derived from a Col-0 × Bur-0 cross, to assess the effect of soil moisture on the expression of each of four quantitative trait loci (QTL) controlling partial resistance. The presence of the Bur-0 allele at the QTL PbAt5.2 resulted in reduced severity only under low irrigation, whereas the Bur-0 allele at QTL PbAt5.1 was associated with partial resistance only under high irrigation. QTL PbAt4 reduced the number of resting spores in infected roots, but was not associated with reduced clubroot symptoms. The results indicated that soil moisture could have consequences for the secondary phase of clubroot development, depending on plant genotype. Future genetic studies may benefit from using combinations of watering conditions during the secondary stage of infection, thus opening up the possibility of identifying genetic factors expressed under specific environmental conditions.