A method combining (1 h) algal photosynthesis inhibition tests and tangential-flow ultrafiltration (TFF) technique (cut-off 1 kDa) was used to determine the effect of humic substances (HS) on acute metal toxicity to Pseudokirchneriella subcapitata. Three “standard” HS (soil and peat humic acids and Suwannee River fulvic acids) at two concentrations (1 and 5 mg/l) and two metals (Zn at 390 μg/l and Cd at 200 μg/l) were studied. Toxicity of Cd and Zn to P. subcapitata was significantly (p<0.05) reduced in the presence of humic acids (HA) but not in the presence of Suwannee River fulvic acids (SRFA). Metal partitioning between colloidal (1 μm–1 kDa) and truly dissolved (<1 kDa) fractions was found to match a decrease of metal toxicity in the presence of HA, but not in the presence of SRFA. The results suggested that HA reduced Cd and Zn toxicity in two different ways: (1) HA decrease the amount of free metal ions. Metal–HA complexes are high molecular weight, relatively stable with regard to metal-exchange reactions and consequently the metals were less bioavailable. (2) HA adsorbed onto algal surfaces, shielded the cells from free Cd and Zn ions. Several possible explanations can be postulated to account for the observed SRFA results: (1) Cd- and Zn-SRFA complexes are thought to be labile (i.e. undergo rapid dissociation); (2) SRFA coagulated, presumably during equilibration, and that coagulation altered metal complexing behavior of SRFA; (3) FA has a lower ability to adsorb on cell membranes at pH>7.