Radionuclide contamination of surface water bodies poses a significant environmental challenge, particularly for low-productivity dystrophic systems where natural self-purification capacity is limited. This study aimed to assess the potential of phytoplankton and bottom sediments as biogeochemical barriers for radionuclides. Laboratory modeling of ⁹⁰Sr, ²³³U, ²³⁹Pu, and ²⁴¹Am accumulation was conducted using samples of Lake Dryazlo (Tver Oblast) water and bottom sediments as a representative dystrophic model system. Sorption onto phytoplankton biomass over a single growing season was estimated at 1.89 × 10⁴, 5.41 × 10⁴, 6.64 × 10⁴, and 4.04 × 10⁴ Bq g⁻¹ dry biomass for ⁹⁰Sr, ²³³U, ²³⁹Pu, and ²⁴¹Am, respectively. Actinide immobilization in bottom sediments depended on mineral composition and microbial community activity. Ammophos addition increased radionuclide removal from the liquid phase by 2–5-fold through enhanced phytoplankton productivity, and promoted actinide fixation via phosphate mineral phase formation and stimulation of anaerobic sulfur- and iron-cycling bacteria. These results demonstrate a viable biogeochemical barrier approach applicable to the decommissioning of radioactive waste storage ponds and remediation of radionuclide-contaminated water bodies.