Abstract <p>This study demonstrates the application of a comprehensive set of mathematical methods—including multivariate statistical analysis, a mathematical model, the JIP-test, and the difference curve method—to analyze the dynamic response of photosystem II (PSII) in <i>Chlorella vulgaris</i> Beijerinck cells exposed to toxicants, specifically cadmium and chromium salts (CdSO₄ and K₂Cr₂O₇) at concentrations of 20 and 50 µM each. During the growth of the <i>Chlorella vulgaris</i> culture in a bioreactor, fluorescence transients were recorded automatically every hour and subsequently analyzed using the integrated mathematical approach. The JIP-test was employed to analyze changes in fluorescence transient parameters over prolonged exposure (~20 h) to the toxicants. Principal Component Analysis was used to reduce dimensionality, and then the curves were classified into three groups based on similarities in curve shape characteristics: (1) control and CdSO₄ (20 µM), (2) K₂Cr₂O₇ (20 and 50 µM), and (3) CdSO₄ (50 µM). The difference curve method was used to examine alterations in the initial segment of the curves, reflecting changes in the oxygen-evolving complex (OEC). A mathematical model was applied to assess the heterogeneity of reaction centers based on OEC activity, calculating the proportions of α- and β-centers, which differ by the presence or absence of a peripheral antenna, respectively. The integrated mathematical approach revealed a decrease in PSII efficiency and OEC activity, while no significant changes were detected in the antenna complex. The use of this complementary set of analytical methods provides a deeper understanding of the mechanisms underlying the adaptation of the photosynthetic apparatus to various stress factors, particularly toxicants.</p>