We test the hypothesis that climate and environmental conditions are becoming favorable for dengue transmission in San Juan, Puerto Rico. Sea Level Pressure (SLP), Mean Sea Level (MSL), Wind, Sea Surface Temperature (SST), Air Surface Temperature (AST), Rainfall, and confirmed dengue cases were analyzed. We evaluated the dengue incidence and environmental data with Principal Component Analysis, Pearson correlation coefficient, Mann-Kendall trend test and logistic regressions. Results indicated that dry days are increasing and wet days are decreasing. MSL is increasing, posing higher risk of dengue as the perimeter of the San Juan Bay estuary expands and shorelines move inland. Warming is evident with both SST and AST. Maximum and minimum air surface temperature extremes have increased. Between 1992 and 2011, dengue transmission increased by a factor of 3.4 (95% CI: 1.9–6.1) for each 1 °C increase in SST. For the period 2007–2011 alone, dengue incidence reached a factor of 5.2 (95% CI: 1.9–13.9) for each 1 °C increase in SST. Teenagers are consistently the age group that suffers the most infections in San Juan. Results help understand possible impacts of different climate change scenarios in planning for social adaptation and public health interventions.