Coastal land reclamation is widely implemented to support coastal development, yet its effects on microbial indicators in coupled surface water–groundwater systems remain poorly understood. This study examined the spatiotemporal variability of four microbial indicators and their environmental associations using 46 months of monthly monitoring (April 2016–January 2020) in eastern Guanghai Bay, China. Total bacterial counts, fecal coliforms, Escherichia coli, and total coliforms were analyzed using multivariate statistical methods. Surface water exhibited elevated levels of fecal indicators, with consistently higher pollution levels in the Xiaoma River than in the Dama River and clear seasonal variation associated with climatic and hydrological conditions. Groundwater showed pronounced spatial heterogeneity: Wells 1 and 2 exhibited relatively elevated microbial contamination, whereas Well 3 maintained persistently low microbial levels under high-salinity and high-alkalinity conditions. These patterns suggest that reclamation may be associated with groundwater microbial distribution through changes in groundwater transport pathways and hydrochemical conditions, while anthropogenic pressures also played an important role in shaping contamination patterns. These findings offer practical insights for groundwater protection and sustainable management in reclaimed coastal environments.