Growing evidence has suggested that ocean warming could cause a decline in marine phytoplankton productivity. However, studies in tropical waters have discovered that evolutionary adaptation of local species to warming and positive response to increasing rainfall could avoid the sharp decline in productivity. Here, the decadal trends of phytoplankton biomass, reconstructed using the biomarkers of brassicasterol (diatoms) and dinosterol (dinoflagellates), showed a 1.5–3 times increase since the 1950s along a large section of the Kimberley coast, north-western Australia. Principal component analysis found that 56% of the phytoplankton variance was linked with climate change-induced increases in sea surface temperature and rainfall associated with increased tropical cyclones, which can enhance nutrient supply favoring phytoplankton growth and production; 20.4% of the phytoplankton variance tended to be related to the Interdecadal Pacific Oscillation through a mechanism of ocean-coast interaction. We empirically predict that the negative impact of rising temperatures on phytoplankton in north-western Australia could be buffered by the increasing tropical cyclones and the coming warm phase of Interdecadal Pacific Oscillation.