Three-year studies (2014–2016) were conducted in Lublin in the south-east Poland. The objects of research were the plants of ten canna cultivars: ‘Aida’, ‘America’, ‘Botanica’, ‘Cherry Red’, ‘La Boheme’, ‘Lucifer’, ‘Picasso’, ‘Robert Kemp’, ‘President’ and ‘Wyoming’. Observations were carried out each year in October. Plants with symptoms of stem and root rot, leaves yellowing and wilt were noticed on the investigated plantations. The plants were studied with regard to photosynthetic activity and also by disease index for all cultivars and statistical analysis was carried out upon them. The effect of disease index on photosynthetic intensity and transpiration was determined after the calculation of Pearson’s correlation coefficient. Infected plants were collected for mycological analysis. The results of mycological analysis showed that canna plants were colonized by Fusarium spp., Sclerotinia spp. and Alternaria spp. Alternaria alternata, Fusarium oxysporum, Fusarium avenaceum and Sclerotinia sclerotiorum predominated among pathogenic species. The best health status and the lowest number of colonies were noticed for plants of cv. ‘Botanica’. The infection of canna leaves by pathogenic fungi has negatively affected the intensity of photosynthesis, transpiration, stomatal conductance and sub-stomatal CO2 concentration and it was largely related to the degree of infestation of specified varieties of canna. The photosynthesis process was limited especially in ‘La Boheme’, ‘Picasso’, ‘Cherry Red’ and ‘President’ cultivars, which were infected most frequently by pathogenic fungi. It was confirmed by negative Pearson’s coefficient.