The aim of the study was to assess the physiological status of Brassica seedlings grown in two types of soils following a single application of smoke water (SW). One soil was contaminated with heavy metals from a local smelter, and another was sandy and poor in nutrients. Three-week monitoring indicated that soil composition was the primary factor affecting chlorophyll fluorescence (CF) parameters, growth, and development of seedlings, and the contaminants affected the plants more than the lack of nutrients. SW aggravated the negative impact of heavy metals, which became visible when the plants transiently suffered from the heavy metal exposure. Most of CF parameters changed suddenly but then the trend reversed indicating that plants gradually adapted to the specific conditions. However, this was not reflected in the final biomass of the seedlings. This might be due to redirection of photosynthates towards protective mechanisms against toxic effects of metals.