The climate in Guaynabo is subtropical, with warm temperatures and high humidity year-round. The municipality is characterized by several rivers and streams that flow into the San Juan Bay, including the Rio Bayamon and the Rio Guaynabo. These water bodies provide important hydrological constituents for the area. Visitors to Guaynabo can enjoy a variety of outdoor recreation opportunities, including hiking and mountain biking in the nearby El Yunque National Forest, kayaking and paddleboarding in the San Juan Bay, and swimming and sunbathing at the many beaches in the region.
Guaynabo receives approximately mm of rain per year, with humidity levels near 78% and air temperatures averaging around °C. Guaynabo has a plant hardyness factor of , meaning plants and agriculture in this region thrive during a short period during spring and early summer. Most plants will die off during the colder winter months.