We investigated the relative importance of metapopulation processes versus environmental conditions for the distribution of freshwater plants in 51 adjacent lakes in southern Sweden. Each lake was surveyed by snorkeling in a zigzag pattern over the littoral zone, and all aquatic vascular plants as well as water colour, Sphagnum‐dominated shore, bottom substrate, littoral zone width and Secchi‐depth were recorded. Data on lake area and altitude was taken from topographical maps. Multiple generalized linear regressions were used to test the significance of factors influencing species number and incidence of specific species in lakes. The best combination of predictor variables for species number was lake area (β=0.52), area of upstream lakes (β=0.23), and height above sea‐level (β=−0.21) (whole model R2=0.52). The presence‐absence patterns of most of the studied species were affected positively by connectivity, measured both as geographical proximity of the lakes and as connection to upstream lakes. The level of effect of connectivity on species incidence was also correlated with life history traits. The distributions of emergent species were less affected by connectivity than those of submerged and floating‐leafed types, reflecting that emergent plants can occur in habitat patches surrounding the lakes. The results indicate that metapopulation processes affect the distribution of freshwater plants, but that their relative importance vary widely among species.