Understanding community assembly in ecosystems is crucial for ecology, yet the interplay between selection and dispersal remains unclear. We examined bacterial and microeukaryotic communities in a dynamic estuarine-coastal ecosystem over six years to investigate the roles of dispersal and environmental selection. Our approach combined species-time relationships (STRs) analysis, a temporal approach focusing on colonization and extinction dynamics, and a process model for community dynamics, revealing insights into the interplay between selection and dispersal along environmental gradients. Both communities showed significant STRs, but their responses varied by taxon and environmental conditions. For bacteria, salinity increased STR exponents, indicating faster richness growth over time, whereas microeukaryotic STR exponents decreased, suggesting distinct assembly mechanisms. Higher salinity reduced bacterial community determinism but heightened it for microeukaryotes, affecting community turnover: microeukaryote turnover decreased with rising salinity due to changes in colonization and extinction, while bacterial turnover increased due to slower dynamics. This study highlights the complex interaction between selection and dispersal, shaped by environmental factors and unique microbial traits, emphasizing the need for tailored conservation strategies in fluctuating coastal ecosystems.