Despite the knowledge of the effects of contaminants on periphyton, information is limited about their natural fluctuations in sensitivity to chemical stress between various months. In particular, the molecular and biochemical mechanisms associated with sensitivity of photosynthesis and its fluctuations remain poorly described. To tackle this lack of knowledge, meta-metabolomics offers a comprehensive picture of the sensitive molecular response preceding the physiological impact. This study aimed to describe changes in the sensitivity of periphyton to chemical stress at different months over one year and a half period, at both the physiological and molecular levels by measuring photosynthetic yield and meta-metabolome responses (targeted and untargeted approaches). Periphyton was colonized for four weeks and then exposed to a range of terbuthylazine concentrations (0.3–30 μg L−1) under controlled conditions for 4 h. Sensitivity was assessed by determining the benchmark doses for the meta-metabolome and photosynthesis, along with the cumulative distribution of aggregated metabolomics signals. The results showed a strong sensitivity shift in the meta-metabolome compared to a smaller shift in photosynthetic yield at different months. This study also confirmed the high sensitivity of the meta-metabolome, as most signals responded before photosynthesis. The annotation highlighted the discrepancies in the molecular response to TBA between the months in terms of metabolite classes (e.g. amino acids, alkaloids, and lipids), their sensitivity, and trends in common classes across months, and correlation to photosynthesis inhibition, notably oxylipins. Overall, this study highlights that the molecular response of the periphyton to chemical stress, and thus toxicity pathways, may differ between the months but can still lead to similar physiological responses.