Evidence now exists that spontaneous mutation rates are non-uniform within genomes across the tree of life, but the causes and consequences of spatiotemporal variation in mutation rates remain uncertain because precise estimates of genome-wide mutation rates are exceedingly rare. To assess the extent to which base-substitution mutation rates vary within the genomes of bacteria with multiple chromosomes, we carried out mutation accumulation experiments paired with whole-genome sequencing (MA-WGS) in three multi-chromosome bacteria, Vibrio fischeri, Vibrio cholerae, and Burkholderia cenocepacia, and two additional MA-WGS experiments in mismatch repair deficient strains of V. fischeri and V. cholerae. We find that in the absence of mismatch repair, base-substitution mutation rates vary in a mirrored wave-like pattern on opposing replichores of the large chromosome of V. fischeri and V. cholerae, where concurrently replicated regions experience similar base-substitution mutation rates. The base-substitution mutation rates on the small chromosome vary less but also tend to follow the patterns of concurrently replicated regions of the large chromosome in both species. We lack a sufficient quantity of base-substitution mutations in the MA-WGS experiments with intact mismatch repair to display significant within genome variation in base-substitution mutation rates, so it is uncertain whether the rates in these studies reflect those of the corresponding mismatch repair deficient MA-WGS experiments. These results support the notion that base-substitution mutation rates vary genome-wide across concurrently replicated regions over the duration of the cell cycle, perhaps owing to the spatiotemporal replication timing program or the conserved nucleoid structure on concurrently replicated bacterial replichores.