Algal assemblages can be highly responsive to environmental changes in recovering acidified lakes. We compared epilithic algal assemblages in boreal lakes during chemical recovery from atmospheric (Killarney Park, Ontario) and experimental (Lake 302S, Experimental Lakes Area, Ontario) acidification to assess the impact of spatial and temporal scale of severe acidification on taxonomic resilience (i.e. recovery rate). Resilience was measured as the distance traveled by lakes in ordination space during pH recovery based on canonical correspondence analysis. Resilience was relatively negligible in the Killarney lakes, suggesting that eight years of experimental acidification in Lake 302S had less impact on biological recovery than did decades of regional acidification. Increases in dissolved organic carbon, dissolved inorganic carbon, and calcium best explained temporal variance of epilithic species abundances in the recovering acidified lakes. In Lake 302S, contrasting trajectories of taxonomic resilience and resistance, i.e. displacement from reference conditions following a perturbation, indicated that ecological factors affecting epilithon differed at corresponding pH levels during recovery and acidification. Our findings reveal that modeling of ecosystem recovery from severe acidification must account for the spatial and temporal scale of the perturbation, and biological delay responses that result in differences between recovery and acidification trajectories.