Understanding the coalescence of materials and microorganisms across pre-configured functional zones in coupled ecosystems is crucial for refining ecological restoration strategies. Deciphering how this coalescence triggers changes in state and functionality is key. However, the emergence of alternative states due to coalescence impacts could lead to abrupt ecological changes near boundaries, with unknown implications. This study focused on a typical coupled ecosystem, constructed wetland (CW), to investigate the impact of coalescence on shifts in aquatic microbial community states. A quantitative method and hierarchical linear models with Bayesian inference were used. Results showed a gradual increase in coalescence from inlet to outlet, with upstream points significantly influencing downstream points (54.13%, 62.35%, 84.03% for each pond). Alternative stable states were found in microbial-mediated nitrogen cycle pathways, leading to a transition from robust denitrification to diminished ammonification and denitrification states. This shift correlated strongly with community cohesion and nitrogen concentration. The observed change in state shift lagged 5% of the total CW length compared to the change in functional states. This research highlights the potential for targeted manipulation of microbial assemblages in CWs for ecological management and restoration.