We analyzed the abundance of benthic algae in nine forested headwater watersheds in south-central Chile to study the relationship between the variability of the abundance of benthic algae and physicochemical parameters and forest cover factors. Between 10 November 2015 and 18 August 2016, we sampled benthic algae and physicochemical parameters in the streams and characterized forest cover factors in each of the study watersheds. We found that physicochemical parameters and forest cover factors have contrasting effects on abundance. More specifically, the following observations were made: (1) maximum diversity and abundance occurred in watersheds covered with Pinus radiata, (2) seasonal ranks did not influence the abundance of benthic algae, (3) benthic algae abundance is controlled by rank dissimilarities in type of vegetation, solar radiation, volume, density age, canopy openness, native forest area, plantation area and harvested area, and (4) regression analysis of genera exhibited significant variability with physicochemical parameters (water temperature, pH, ammonium, nitrate, phosphorus, solar radiation) and forest cover factors (volume, density, age, native forest area, plantation area and harvested area); however, these effects were not seen in all genera. Factors related to the benthic algae compartment showed the highest sensitivity to forest cover, emphasizing their value as biological indicators of water quality and stream ecological integrity.