The chemical speciation of trace metals in natural waters has important implications for their biogeochemical behavior. Trace metals are present in natural waters as dissolved species and associated with colloids and particles. The complexation of one trace metal (Cd and Zn at 200 and 390 μg/l respectively) with a green alga Pseudokirchneriella subcapitata in colloid-free algal culture medium and in presence of colloidal humic substances (HS) is presented. The influence of the nature of colloids was also addressed using three “standard” HS: fulvic acid (FA) and, soil (SHA) and peat humic acids (PHA). The chemical speciation model, MINTEQA2, was used to simulate the influence of pH and standardized culture medium on metal association with humic substances. The model was successfully modified to consider the differences in the metal complexation with fulvic (FA) and humic acids (HA). The deviations of concentrations of metals associated with HS between experimental results and model predictions were within a factor of ≈2. The results of speciation model highlight the influence of the experimental conditions (pH, EDTA) used for alga bioassay on the behavior of Cd and Zn. The computed speciation suggests working with a pH buffered/EDTA-free mixture to avoid undesirable competition effects. The behavior of Cd and Zn in solution is more strongly influenced by HS than by alga. Metal–HS associations depend on metal and humic substance nature and concentration. Cd is complexed to a higher extent than Zn, in particular at larger HS concentration, and the complexation strength is in the order FA < HA.