The acidification chronology of Gr. Arbersee (Bavarian Forest, Germany) was studied by means of subrecent diatom, and chrysophyte as well as metal (Al, Cu, Cd, Mg, Ca) stratigraphies. pH was inferred by diatom assemblages so that the simultaneous effects of acid and accompanying metals on chrysophytes could be evaluated. The occurrence of seven dominant Mallomonadacean taxa was related to the environmental variables by applying Spearman rank correlation and factor analysis. During the post-glacial period of natural acidification, increases in organic carbon and declining pH favor Mallomonas crassisquama and disfavor M. heterospina and M. caudata. Potentially toxic metals (Al, Cu, Cd) and the two alkaline earth metals (Ca, Mg) impact the occurrence as well. Although acidity appears to be also the major driving force during the recent acidification period, the occurring Mallomonadacean species may be differentiated by their tolerance toward Al and heavy metals.