As shown by fluorescence monitoring of dissolved organic matter, amino acid L-Trp can be present in natural water. The consequences of the presence of L-Trp at low concentrations in surface water systems are not yet established for hydrobionts. Studying the physicochemical patterns, as well as their relationships to the bioeffects of L-Trp solutions in the low concentration range, can provide new and important information regarding the unknown effects of L-Trp. The self-organization, physicochemical properties, fluorescence, UV absorption, and action of L-Trp solutions on Paramecium caudatum infusoria, Chlorella vulgaris algae were studied in the calculated concentrations range of 1 × 10−20–1 × 10−2 mol/L. The relationship between these phenomena was established using the certified procedures for monitoring the toxicity of natural water and wastewater. It was shown for the first time that aqueous solutions of L-Trp are dispersed systems in which the dispersed phase (nanoassociates) undergoes a rearrangement with dilution, accompanied by coherent changes in the nanoassociates’ parameters and the properties of systems. The non-monotonic concentration dependence of fluorescence intensity (λex at 225 nm, λem at 340 nm) is in good agreement with the data on the nanoassociates’ parameters, as well as with both the physicochemical properties of the systems and their bioassay results.