Coastal nitrogen cycling is shaped by the interaction of physical mixing, nutrient inputs, and microbial community processes, yet their coupled effects remain insufficiently resolved in tropical coastal systems. Here, we investigated dissolved inorganic nitrogen speciation, pico-nano-phytoplankton composition, and nitrogen uptake dynamics across contrasting environmental regimes in Xiaohai Lagoon, Qinglan Port (Q), and Gaolong Bay (G) along the eastern Hainan coast. Weakly flushed southern Xiaohai Lagoon exhibited pronounced nitrite accumulation coincided with long residence times. In contrast, aquaculture-impacted and well-mixed regions (Q, G) displayed elevated NH₄⁺, shifts toward Synechococcus dominance, and consistently strong NH₄⁺ uptake preference. Across the system, phytoplankton favored NH₄⁺ (RPI > 1), with spatial variability structured by salinity gradients and community composition. Structural equation modeling revealed nitrogen preference was primarily shaped by biological controls in stagnant southern Xiaohai waters, whereas regions influenced by stronger physical mixing and aquaculture nitrogen inputs exhibited multi-factor regulation. Our findings show how environmental forcing modulates nitrogen speciation and phytoplankton nitrogen use strategies, providing mechanistic insight into nitrogen uptake functioning and eutrophication vulnerability in tropical coasts.