This work presents a case study accompanied by an analysis of potential reasons for fish mortality in the lower Oder River during an ecological disaster in August 2022. Changes in physicochemical water quality indicators indicate that fish and benthic organism death was likely due to the creation of hypoxia. The research also highlighted the trophic threats to the studied Oder River section linked to the disaster. The disaster occurred in the upper and middle Oder River, extending to the lower stretch. A physicochemical analysis of water samples revealed that the fish and organism death in the estuarine section was mainly due to reduced dissolved oxygen, caused by the decomposition of organic matter from the upper river sections. This was reinforced by high temperatures and low water levels. The negative trophic consequences of the described ecological disaster for the lower section of the Oder River may be long-term. Over thirty years of monitoring showed threats of excess biogenic compounds, organic matter, and bacterial contamination. Despite decreasing nitrogen and phosphorus, significant phytoplankton blooms implied internal nutrient sources. Considering climate change and the poor trophic status, recurrent disasters and deteriorating conditions are anticipated. Mitigation requires continuous monitoring, limiting the nutrient input (especially phosphorus), and preparing for extreme events. Geotechnical methods in the lower river can improve oxygen levels and fish survival.