In light of limited research into the relationship between the macroscale distribution and dynamic changes of microplankton in the shallow Bohai Sea, here we used flow cytometry to analyse samples collected from the Bohai Sea channel in winter and summer. Results showed that the average of both viral abundance (VA) and bacterial abundance (BA) were lower in winter (3.61 × 107 and 1.84 × 106 cells/mL, respectively) than in summer (7.47 × 107 and 5.05 × 106 cells/mL, respectively). At all 16 stations, VA was one order of magnitude greater than BA, with a positive relationship between one another. In the horizontal distribution, variations in VA and BA followed a similar trend, and both were obviously higher near-shore than offshore. In the vertical distribution, variations in both VA and BA did not show a clear relationship with water depth. VA and BA in summer were 2.1 and 2.7 times those in winter, respectively. Spearman correlation analysis showed that both VA and BA were correlated with the concentration of PO4-P in winter (positive) and NO3-N in summer (negative). Additionally, BA showed a negative correlation with salinity. It is clear that the macroscale distribution of these two kinds of microbes in the Bohai Sea is related to seasonal variation and nutrient availability.