Background: Dengue is one of the most important mosquito-borne viral diseases in Mexico, where transmission is shaped by complex interactions among environmental, demographic, urban, land-use, and climatic conditions. However, long-term national ecological analyses integrating these factors remain limited. This study evaluated ecological associations between environmental, demographic, urban, land-use, and climatic indicators and dengue incidence trends in Mexico from 1990 to 2021. Methods: A national ecological time-series study was conducted using annual aggregated data obtained from official public databases. Dengue fever and severe dengue incidence rates were analyzed in relation to environmental, land-use, urban, demographic, and climatic indicators. Exploratory simple and multiple linear regression analyses were performed, and autoregressive integrated moving average models with exogenous variables (ARIMAX) were used to evaluate temporal associations while accounting for autocorrelation. Results: In simple regression analyses, urban population, population density, renewable internal freshwater resources, forest area, and average annual temperature were significantly associated with dengue incidence. For severe dengue, renewable internal freshwater resources showed the highest explanatory capacity in simple regression analyses (R² = 0.33). In multivariable models, forest area remained positively associated with severe dengue incidence (β = 64.29; p = 0.006), whereas renewable internal freshwater resources showed an inverse association (β = −0.087; p = 0.002). After accounting for temporal autocorrelation, none of the environmental or demographic indicators remained statistically significant in ARIMAX models; however, renewable internal freshwater resources showed the strongest association with severe dengue incidence (p = 0.062). The severe dengue model included a significant first-order moving-average component (MA(1), p < 0.001), indicating short-term temporal dependence in annual incidence rates. Conclusions: Environmental, demographic, urban, land-use, and climatic indicators were associated with long-term national dengue incidence trends in Mexico. Renewable internal freshwater resources emerged as one of the most consistent ecological indicators across analyses, highlighting the relevance of water availability and management within integrated dengue prevention strategies. The temporal dependence observed for severe dengue suggests that ecological time-series analyses may contribute to improving epidemiological surveillance and generating hypotheses for future regional studies.