This study was conducted with using chlorophyll a fluorescence (indicated as photosynthetic activity) to examine the toxic effect of 96 h exposure of heavy metals and herbicides on the benthic diatom Nitzschia sp. which was isolated from pristine sediment in Pamquat Harbour, Nova Scotia, Canada. Samples of benthic diatom were exposed to 0, 0.01, 0.1 and 1 mg L?1 of copper, 0, 1, 10 and 100 mg L?1 of chrome (VI), 0, 2.45, 24.5 and 245 mg L?1 of paraquat dichloride, and 0, 4.37, 43.7 and 437 mg L?1 of alachlor during 96 hours. The effective quantum yield of photochemistry (ΔF/Fm’) was evaluated by subjecting light acclimated samples to saturating pulses of light using a pulse amplitude modulated (PAM) fluorometer. The impact of heavy metals on Nitzschia sp. photosynthesis was not severe in < 1 mg L?1 but in the high concentrations (> 1 mg L?1) clearly increased toxic stress during 96 h. Herbicides had a limited impact during the exposure period but clearly increased stress on the benthic diatom with increasing concentrations. Acute response of Nitzschia sp. to selected heavy metals and herbicides was characterized, and the capacity of a benthic diatom to tolerate and recover from toxic stress was assessed.