Sand spits are common in wave-dominated environments; with enough sand supply, they can evolve to affect circulation and navigation in channels or inlets. The focus of this paper is on the navigation channel of the Sisal Port, located on the northwestern Yucatan Peninsula (YP) coast, where a sand spit grew and was monitored from its formation (June 2018) until navigation was practically blocked (November 2018). The YP coast is characterized as being microtidal, with significant wave heights ranging from 0.1 to 0.4 m (April to September), and in the presence of high energy events (cold fronts and storms), waves can reach heights of up to 2.5 m offshore at 10 m depth (October to February). Prior to the beginning of UAV surveys, we used photos (June–July 2018) from a stationary field camera and hydrodynamic data from models (WaveWatch III for waves and MARV software for tidal levels) to generate a qualitative description of the sand spit in the channel. Combining products from UAVs flights (DEMs) and hydrodynamic measurements (wave energy flux), we characterized the behavior and response of the sand spit, from its formation near the jetty head, through its consolidation in October 2018, to when a cold front with H_S ∼2.5 m breached it in mid-November. The results show that spit formation takes place during calm conditions (e.g., periods dominated by sea breezes), and depending on the energy threshold of high energetic events, this new spit will consolidate or be breached. Migration of the spit is related to overwash events and changes in wave direction. The presented methodology provides a well-rounded tool for characterizing the morphological behavior of spits on a shallow coast, which can be useful for improving coastal management.