Marine mammals in subtropical coastal habitats are sentinels of the health of the ecosystem and offer important ecosystem services. They rely on prey that pursues feeding opportunities, while both avoid unfavorable conditions. In many cases, these predator-prey dynamics fluctuate seasonally and are regulated by lunar, tidal, and/or diel cycles (hour). However, these rhythmical patterns may vary under different seasonal conditions. Bottlenose dolphins (Tursiops truncatus) in the Ensenada de La Paz in Baja California Sur, Mexico, were detected acoustically over the course of an annual cycle on 21 separate occasions, covering 640 h from June 2017 to May 2019. The presence of bottlenose dolphins was examined using Generalized Additive Models (GAM) including variables that are related directly to their habitat (direct variables: hour, distance, depth) and to their prey (indirect variables: SST, moon phase and tides). Seasonal differences in the presence of bottlenose dolphins were influenced more by indirect variables (explained deviance: 34.8% vs. 37.7%). Hourly acoustic detections occurred less frequently when SST exceeded 27.4 °C (Aug–End of Nov.) and more frequently at moderate temperatures (22.7 °C to 26.3 °C) in May through July. Moreover, bottlenose dolphins were detected more frequently during waning and new moon phases, at the onset of flood and ebb tides, and during day (04:00 to 20:00). The seasonal differences in acoustic detections rates were highlighted by the global GAM and hierarchical clustering. The strong seasonal pattern indicated possible interactions with rhythmic pattern of bottlenose dolphins. Four candidate variables (SST, moon, tide, and hour) were tested for plausible interaction terms additional to their individual consideration, out of which only hour changed significantly between seasons. The patterns of presence likely increase feeding opportunities or may favor other behaviors such as socializing, resting, or nursing. These might prove responsible for the distinct occurrence and hourly patterns of bottlenose dolphins.