Surface waters function as ecological niches where Salmonella enterica can persist and disseminate to fresh produce production systems. We examined the genomic characteristics of S. enterica serotypes Agona (n = 86), Braenderup (n = 47), Muenchen (n = 53), and Panama (n = 69) isolates from surface waters in Chile, Mexico, and Brazil between 2019 and 2022. Mexican isolates consistently displayed a higher occurrence of genotypic antimicrobial resistance (AMR) than Chilean and Brazilian isolates. All S . Agona isolates exhibited the presence of fosA7.2, while qnr819 emerged as the predominant AMR gene (ARG) among S . Braenderup isolates. S . Muenchen isolates from Chile displayed an absence of any ARGs, while those from Mexico and Brazil predom inantly carried qnr819. Among S . Panama isolates from Chile, aadA1, floR, sat2, and tet(8) were the most prevalent ARGs, whereas those from Mexico and Brazil harbored tet(A), and floR and tet(A) as the leading ARGs, respectively. ARG sharing among isolates and ARG co-occurrence within individual isolates were prevalent across countries and serotypes. All isolates containing integrons exhibited genotypic multidrug resistance. The principal coordinates analysis reveals distinct clustering patterns based on country, serotype, number of ARGs per isolate, and plasmid and integron presence/absence. The whole-genome phylogenetic analysis demonstrates clear clusters, each associated with their respective countries. However, a notable exception was observed with one S . Agona isolate from Brazil closely related to two isolates from Chile, differing by only 18 and 19 single-nucleotide polymorphisms, respectively.