To cascading linkage between environmental disturbance, community assembly, and functional output in coastal ecosystems under rainfall forcing, We conducted a 23-day time-series survey (May–June 2024) in a typical semi-enclosed Daya Bay in the South China Sea. The results showed that continuous rainfall significantly reduced salinity through freshwater input while enhancing nutrient loading, thereby restructuring coastal environmental conditions at the daily scale. Environmental responses exhibited clear temporal lags, with salinity declining persistently while nutrients accumulated over 1–3 days, forming a coupled “physical disturbance–nutrient pulse” process. Community assembly inferred by the iCAMP model showed that homogeneous selection became prevalent during continuous rainfall, but stochastic processes (ecological drift) dominated during the other rainfall stages, demonstrating that rainfall could rapidly shift assembly regimes, with salinity decline acting as a key driver of enhanced environmental filtering. Community analyses revealed pronounced successional dynamics in Pseudo-nitzschia assemblages under rainfall disturbance, shifting from single-species dominance to multispecies coexistence and subsequent re-dominance. At the species level, environmental filtering during continuous rainfall preferentially retained euryhaline taxa, particularly the toxigenic species P. multistriata. During the subsequent salinity recovery phase, stochastic processes facilitated rapid population expansion of dominant taxa. DA dynamics showed a strong positive correlation with Pseudo-nitzschia cell abundance, with peak concentrations lagging behind rainfall and occurring during the recovery phase. Integrating community assembly and functional responses, we propose a two-stage ecological mechanism: “deterministic selection–stochastic expansion.” Continuous rainfall imposes environmental filtering that selects for toxigenic taxa, while subsequent stochastic expansion drives population growth and DA accumulation. This finding highlights that toxin risk is not a direct response to environmental forcing but rather an emergent property of community assembly history and mechanisms.