Recruitment is the addition of individuals to a population that generally occurs in the early juvenile phase, which is key to understanding the dynamics of reef fish communities. Through visual censuses in three climatic seasons (dry, rainy, and northerly winds) between 2017 and 2020, the analysis of seasonal and interannual variations in the abundance of fish recruits in a reef lagoon (Mahahual, Quintana Roo, México) was carried out. Temporality was analyzed using average recruit density graphs and multivariate analyses (multivariate ANOVA, ANOSIM, and RDA) to assess composition differences between year and season levels. A total of 9326 recruits were registered, belonging to 36 species and 8 fish families. The Labridae had the greatest number of recruits, followed by Pomacentridae and Scaridae. The recruits were more abundant in the dry season when the average temperatures were 27.50–27.87 °C; meanwhile, they presented a lower abundance in the northerly wind season when the temperature was lower (26.7 °C). The most abundant species was Thalassoma bifasciatum (138.72 recruits/100 m2), followed by Abudefduf saxatilis (100.05 recruits/100 m2) and Halichoeres bivittatus (45.94 recruits/100 m2). The multifactorial ANOVA for the average density and the ANOSIM for the composition of recruits did not show significant differences for the year factor, but they did for the season factor. RDA indicated that the greatest average dissimilarity existed between the dry season and the other two climatic seasons. The results of this study highlight the importance of recruitment during the warm months and the refuge offered by the lagoon for the maintenance of reef fish populations.