The influence of estuarine zonation in a coastal lagoon on the population variability of exploited penaeid shrimps Farfantepenaeus aztecus, F. brasiliensis, F. duorarum and F. notialis (Crustacea: Decapoda) at the ‘Ría Celestún’ Biosphere Reserve, Mexico, was evaluated. Monthly samples of shrimp and environmental factors were taken throughout 1997 and 1998 in three zones (seaward, middle, inner) of Celestún lagoon. Salinity and aquatic vegetation biomass exhibited a clear spatial heterogeneity of habitat. A total of 20,757 shrimps were collected mainly at the seaward zone, which registered the highest salinity and aquatic vegetation biomass. This revealed the critical contribution of the seaward zone as the most suitable habitat for shrimp populations, mainly for recruits. Results support the implementation of spatially-explicit management strategies, such as the closure of the seaward zone for fishing activities. The significant relationship between the recruits and the subsequent abundance of shrimp in the lagoon also support this operational measure.