Conventional photosystem II (PSII) herbicides applied in agriculture can pose significant environmental risks to aquatic environments. In response to the frequent detection of these herbicides in the Great Barrier Reef (GBR) catchment area, transitions towards 'alternative' herbicides are now widely supported. However, water quality guideline values (WQGVs) for alternative herbicides are lacking and their potential ecological impacts on tropical marine species are generally unknown. To improve our understanding of the risks posed by some of these alternative herbicides on marine species under tropical conditions, we tested the effects of four herbicides on the widely distributed diatom Chaetoceros muelleri. The PSII herbicides diuron, propazine, and tebuthiuron induced substantial reductions in both 24 h effective quantum yields (ΔF/Fm') and 3-day specific growth rates (SGR). The effect concentrations, which reduced ΔF/Fm' by 50% (EC50), ranged from 4.25 µg L-1 diuron to 48.6 µg L-1 propazine, while the EC50s for SGR were on average threefold higher, ranging from 12.4 µg L-1 diuron to 187 µg L-1 tebuthiuron. Our results clearly demonstrated that inhibition of ΔF/Fm' in PSII is directly linked to reduced growth (R2 = 0.95) in this species, further supporting application of ΔF/Fm' inhibition as a valid bioindicator of ecological relevance for PSII herbicides that could contribute to deriving future WQGVs. In contrast, SGR and ΔF/Fm' of C. muelleri were nonresponsive to the non-PSII herbicide haloxyfop at the highest concentration tested (4570 µg L-1), suggesting haloxyfop does not pose a risk to C. muelleri. The toxicity thresholds (e.g. no effect concentrations; NECs) identified in this study will contribute to the derivation of high-reliability marine WQGVs for some alternative herbicides detected in GBR waters and support future assessments of the cumulative risks of complex herbicide mixtures commonly detected in coastal waters.