Seasonal variation in N:P ratios and shifts in nutrient limitation can provide important implications for nutrient management in aquatic ecosystems. However, management strategies that consider seasonal or storm-driven impacts on receiving water are limited. We analyzed the long-term monitoring data from two Australian rivers with contrasting nutrient stoichiometry: the Logan–Albert River (mean TN:TP ratio of 5:1) and the Hawkesbury–Nepean River (mean TN:TP ratio of 40:1). We also investigated their nutrient limitation conditions along upstream–downstream gradients over six months under dry and wet conditions using nutrient enrichment algal bioassays, and identified nutrient thresholds associated with near-saturating algal responses. In both rivers, wetter and warmer months were characterised by declining TN:TP ratios, lower TN concentrations, and higher TP concentrations. However, lower TN:TP ratios under wet conditions in the Logan–Albert River intensified N limitation. In contrast, reduced TN:TP ratios in the Hawkesbury–Nepean River weakened P limitation and promoted N and P colimitation. These contrasting responses indicate that similar seasonal TN:TP ratio shifts can produce divergent ecological outcomes for rivers with different nutrient limitation status. Bioassay-derived nutrient thresholds for nitrogen and phosphorus were also identified at 90%, 95%, and 99% saturation levels, providing guidance for setting water quality objectives in these rivers. Our findings emphasize the need to account for temporal variability in nutrient limitation. Targeting nutrient inputs during critical periods, such as dry seasons in N-limited systems and wet-weather events in P-limited systems, may improve management effectiveness in rivers with similar seasonal N:P dynamics.