Like all headwater systems, springs have been increasingly modified by multiple land uses, but the effects of these modifications on species diversity and community composition are poorly understood. We assessed the consequences of forestry-related disturbance (mainly draining) on benthic macroinvertebrate and bryophyte diversity and community composition in boreal springs. We used predictive modeling (BEnthic Assessment of SedimenT [BEAST]), indicator species analysis, and descriptive statistics on data from 55 near-pristine reference springs and 20 modified (test) springs spanning 3 ecoregions (hemiboreal to middle boreal) in Finland. Invertebrate and bryophyte communities were relatively similar between the reference and test springs. BEAST identified deviation from the reference condition in 9 and 10 sites based on benthic macroinvertebrates and bryophytes, respectively. These sites were identified mostly as possibly different from reference, with the exception of a few seriously degraded springs with low levels of groundwater flow. Indicator species for both reference-condition and test springs included spring-preferring and ubiquitous taxa. Bryophyte richness was lower in test than in reference springs, but no significant differences were detected for macroinvertebrate richness. Red-listed species were more common in reference than in test springs. Our results suggest that, despite only moderate effects on community composition, anthropogenic disturbance impoverishes spring fauna and flora and causes a decline of spring-preferring red-listed species. Restoration will be necessary to preserve biodiversity in springs, but benign methods should be used to avoid further disturbance to biota, particularly red-listed spring specialists.