The species richness is a major marker of gut health directly affecting feed efficiency (FE). We previously demonstrated that dairy calves receiving drinking water from birth (W0) had greater BW and FE than those first receiving drinking water at 17 d of age (W17). The objective of this study was to examine the impact of offering drinking water from birth on species richness and the abundance of bacterial communities in fecal microbiome of dairy calves. Thirty newborn Holstein heifer calves were randomly assigned (n = 15) to W0 and W17, fed with pasteurized milk, and weaned at 6 wk of age. Fresh feces were collected directly from the rectum at 2, 6, and 10 wk of age. The DNA was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq system. The sequences were clustered into operational taxonomic units (OTU) with a 99% similarity threshold. Treatment effects on species richness were analyzed with MIXED procedure in SAS including treatment and time (fixed effects), and calf (random effect). Treatment effects on relative abundance of the 25 most abundant OTUs were analyzed using GENMOD procedure in SAS (distribution = Poisson). At 2 wk of age, W0 had a greater number of observed species (P = 0.033) and species richness (the Chao1 index, P = 0.042) than W17. The number of species and the Chao1 index increased over time (P < 0.01) and became similar between W0 and W17 at 10 wk of age. At 2 wk of age, relative abundance of Bacteroides in W0 was 2.5-fold higher than W17, whereas Lachnospiraceae and Streptococcus in W17 were 2.0 and 8.0-fold higher than W0 (P < 0.04), respectively. At 6 wk of age, Streptococcus, Fecalibacterium and Bifidobacterium in W0 were 3.0, 7.0 and 5.0-fold greater than W17, respectively (P < 0.04), whereas Bacteroides in W17 was 2.0-fold greater than W0. At 10 wk of age, Succinivibrio and Alloprevotella in W0 were 4.5 and 5.5-fold greater than in W17, respectively (P < 0.01). Offering drinking water from birth was related to increased species richness in the gut of neonate calves. Higher abundance of some beneficial OTU (Bifidobacterium, Fecalibacterium, Succinivibrio) could partly contribute to the improved performance of W0 calves.