The source of nutrients that sustains abundant benthic primary productivity on Western Australian coastal reef systems is unknown, but it is possible that cycling between organic matter production and remineralisation contributes and may be enhanced by variations in the magnitude of physical forcing. We have used a 5-year nitrate dataset collected at weekly, daily and hourly temporal scales to investigate dynamics and supply mechanisms in Marmion Lagoon, Perth, Western Australia. Nitrate concentrations were variable over short time scales (hours) and formed pulses of elevated nutrient concentrations. On average, nitrate concentrations were highest during the high energy winter period (June to August) and scant wave data (June to August 1984) suggest a general correlation between wave activity and nitrate concentration. While it was not possible to definitively link variations in nitrate to wave forcing, increased energy may have promoted carbon recycling and nitrate release (possibly through abrasion of macroalgae, resuspension of detrital material or enhanced pore water exchange). Rapid uptake suggests that the nitrate pulses observed here may help sustain primary productivity in this shallow high energy environment. High temporal (hourly) variability suggests future surveys must sample at a frequency adequate to isolate long-term temporal trends from short-term background variations.