Multicell constructed wetlands (MCWs) on lakeshores are a prospective treatment technique. However, the factors affecting the nutrient removal performance of lakeshore MCWs at the field scale are unclear. This study chose a field-scale lakeshore MCW with the highest mass removal efficiency (approximately 49,175.12 mg m−2 day−1) for total nitrogen removal in the wet season to investigate the response of nitrogen removal and microbial distribution to seasonal shock nutrients load. The mass loading rates in the wet season were as high as 43~72 times over those in the dry season. Hence, a storage pond (SP), as a forebay retention cell, was necessary to mitigate the shock loads of the influent, which is beneficial to nitrogen removal of the MCW system. The two major genera in the sediments are heterotrophic nitrification−aerobic denitrification bacteria, and the abundance and species of the nitrogen-related functional genera were higher in the wet season than the dry season. According to the results of redundancy analysis, the hydraulic residence time (29.4%, F = 2.2, p < 0.1) and hydraulic loading rate (85.9, F = 36.5, p < 0.05) were the major factors explaining microbial community variation, instead of environmental factors (temperature, pH, and dissolved oxygen). The shock loads of influent and the periodic saturation in sediments contributed to a complicated oxygen and nitrogen nutrient exchange environment resulting in higher abundance and species of nitrogen-related microbes, which is beneficial to nitrogen removal in lakeshore MCWs. The results provided a scientific basis for the optimal design of constructed wetlands on lakeshores.