There are gaps in what is known about the patterns of gastropod shell use by hermit crabs in Brazilian lagoon areas, especially in Northeastern Brazil. However, this is important because the understanding of selection patterns provides information on life history and eco‐evolutionary conceptions of paguroids. The present study investigated the use of gastropod shells occupied by Pagurus criniticornis and Clibanarius sclopetarius in a coastal lagoon seasonally connected to an estuary and to the sea, correlating eco‐evolutionary aspects and hydrodynamic characters. The study was carried out between February 2013 and January 2014. Hermit crabs and their shells were identified and measured (hermit crabs’ cephalothorax shield length and width, major propodus length and height, weight, shell total length and width, shell aperture length and width). Partial least squares regression was used to analyse the morphometric data. Additionally, a multinomial proportions test was performed to infer patterns (inter‐/intra‐specific) of shells’ occupation. Hermit crab species occupied a total of 13 types of shells, predominantly those of Neritina virginea (67.83%). The shell weight was the most important determinant of shell occupancy in the morphometric model (variable importance in projection >1). The proportions of N. virginea shells used were similar in both species of hermit crabs, except between the sexes of P. criniticornis. Presumably, the high utilization rate of N. virginea shells is related to its abundance and dispersal, and to the shells’ suitability for hermit crabs, which is reflected by the morphometric model, as well as by the hydrodynamics of the lagoon‐estuarine environment. The relative occupation of different types of shells for each species of hermit crabs studied appears to be associated with regulation by inter‐/intra‐specific competition, which fosters the co‐occurrence of those populations. These results endorse coastal lagoons as a refuge and recruitment area for aquatic fauna. In addition, it highlights a challenge in the management and conservation of paguroid species whose population dynamics depend on the resources coming from the Gastropoda community.