This study investigated the spatial variation in total benthic algal biomass and within cyanobacteria, green algae, and diatoms in sub-Arctic ponds. Additionally to more widely used explanatory variables, snowmelt and ice duration were considered as their importance on algal communities is poorly understood. The data comprised algal biomasses from 45 sub-Arctic ponds in the Finnish Lapland. A generalized linear model and hierarchical partitioning were used to identify the significantly influential variables. Cyanobacteria were the most abundant algal group. Trace elements (e.g. Fe, Al, and Mn) were the most significant explanatory variable group in explaining algal biomasses. Macronutrients apart from K were found insignificant in all models. There were positive relationships between some algal biomasses indicating no strong competition between them. Snow and ice variables were found insignificant for all models, but they could have an important secondary role on algal communities. The results highlight the importance of trace elements in shaping algal biomasses in sub-Arctic ponds and thus their wider use in research can be advocated to better understand the productivity of nutrient poor and acidic waters in sub-Arctic regions. Focussing on benthic algal biomasses and the chemical composition of sub-Arctic freshwaters provides important information on the aquatic primary production.