We investigated shifts in nekton assemblages in coral reef, seagrass, and mangrove habitats that coincided with a coral bleaching event in June 2016. The study was conducted in May 2016 (prebleaching), July 2016 (bleaching), October 2016 (4-mo postbleaching), and February 2017 (7-mo postbleaching) in relatively undisturbed coastal areas in Busuanga, Palawan, western Philippines. We used triangular trap nets to capture nekton samples from each habitat. In coral reef and mangrove habitats, there were increases in nekton abundance and biomass from the prebleaching to the bleaching period. After the bleaching event, however, there were reductions in nekton abundance and biomass at the coral reefs until 7-mo postbleaching. Species composition changed at all sites where shifts in dominant species, habitat affinity, and trophic category were observed. The postbleaching increase in nekton abundance in mangroves coincided with the decreased nekton abundance in the coral reef, suggesting a cross-habitat movement, likely due to the reduced suitability and/or food in the bleached coral reef. The changes in the nekton assemblage may also have been due to seasonal fluctuations in environmental parameters, especially salinity. Our study presents evidence of the possible role of coral bleaching or seasonal changes on cross-habitat movements of nekton assemblages, which can be inferred as an indicator of disturbance. The presence of adjacent vegetated habitats may provide refuge for the affected nekton assemblage of the coral reef.