Water chemistry and bacterioplankton were analysed for two subalpine rivers, River Kidisjoki and River Utsjoki, in northernmost Finland. The data set is based on continuous runoff measurements and weekly chemical and biological samples. The data were collected during the open water period, from May to October, in year 2000. The runoff patterns during the summer were similar in the two rivers at though the size of the catchments is very different (the catchment of River Utsjoki 1,520 km2 and of River Kidisjoki 22 km2). For both rivers, variations in runoff were followed by variations in the water quality and bacterial densities. The measured chemical concentrations were usually the highest in the headwaters of river Kidisjoki, while in the lower Kidisjoki they were clearly lower than in Utsjoki. Bacterial densities were on average highest in Utsjoki and the strongest relationships between water chemistry and bacteria were found in Kidisjoki. Both the chemical concentrations and bacterial densities were low in the two rivers when compared to other studied rivers in northern Finland.