Total ammonia nitrogen (TAN) is a ubiquitous and critical pollutant in global surface waters. In China, regulatory oversight largely relies on static standard limits, often overlooking the influence of environmental factors on ammonia toxicity. Based on large-scale monitoring data from seven major river basins across China from 2021 to 2024, this study employed pH- and temperature-dependent Local Water Quality Criteria (LWQC) to identify the spatiotemporal decoupling between TAN concentrations and Risk Quotients (RQs). The results reveal a “double-peak” seasonal pattern in TAN concentrations nationwide, namely a primary peak in winter (December to February) and a secondary peak in summer (June to August), driven by low flow during the dry season and rainfall-induced non-point source runoff, respectively. Crucially, the study confirms a significant “concentration-risk paradox”: while TAN concentrations are highest in winter, ecological risk remains at an annual low due to the protective effect of low temperatures on toxicity. Conversely, despite lower total concentrations in summer, high temperatures and elevated pH trigger a sharp decline in LWQC and a surge in the proportion of highly toxic un-ionized ammonia (NH₃), marking summer as the peak period for ecological risk. Comparative analysis indicates that approximately 61.43% of river sections meeting the current Grade III water quality standards remain in a high-risk state. This underscores the inadequacy of static standards in providing sufficient protection during sensitive seasons. We suggest that water environmental management should shift from “concentration-based compliance” to “risk-based management,” implementing differentiated TAN control strategies specifically targeting the sensitive summer window.