Anthropogenic pressures on coral reefs are intensifying worldwide. Coral reefs are thought to be among the most vulnerable marine ecosystems to environmental change and localized stressors associated with human activities. Among localized stressors, suspended sediments are a growing concern, particularly for fringing coral reefs exposed to increased coastal development and land use. Due to climate change-driven intensification of storms and extreme rainfall, suspended sediment events are expected to increase in frequency and severity. Intense rain events can come in different regimes, for example, sustained rainfall that generates continuous suspended sediment input or intense storms followed by dry periods that create intermittent exposures. Due to this, suspended sediment events vary considerably in their duration and frequency, yet the biological consequences of these different regimes remain largely unexplored. We addressed this question using juvenile false clownfish (Amphiprion ocellaris), as they are a site-attached species, and exposed them to three regimes: control, chronic, and pulsed. Following exposure, we measured: (1) metabolic rates, (2) gill histology quantifying epithelial damage, (3) RNA-seq of brain, eye, and gill tissue, and (4) proteomic analysis of the gills. Our findings show significant changes in the metabolic rates, where chronic exposure resulted in lower maximum metabolic rate and higher routine metabolic rate, as well as greater epithelial damage. Changes in gene expression between treatments, especially in the gills, were observed, with a strong clutch effect. There were also differences in protein composition between treatments. Together, these findings indicate that the temporal pattern of suspended sediment exposure strongly shapes physiological and molecular stress responses in coral reef fish, with prolonged exposure imposing substantially greater impacts than intermittent sediment pulses.