Environmental factors, such as light intensity and exposure to contaminants, may significantly influence the lipid composition of algae in periphytic communities. In this study, we investigated the joint effects of dodecylbenzyldimethylammonium chloride (BAC 12), as biocide, and light photoperiods on the polar lipidome of a freshwater biofilm. Exposure to BAC 12 in a microcosm experiment increased the heterotrophic compartment, while phototrophic organisms were severely affected, with corresponding shifts in lipid composition. The overall decrease in polyinsaturated fatty acids suggested a significant impact of the biocide on biofilm microalgae. However, it was difficult to distinguish the influence of light from that of contamination, as there was no observable effect of photoperiod on conventional fatty acid determination. Thus, the molecular species compositions of both glycolipids and phospholipids were explored in additional multivariate analyses. The results suggested that certain molecular species can serve as more specific markers of light duration at the biofilm scale, independently of the chemical pressure caused by other pollutants.