The bioaccumulation of PAHs and metal elements in the indigenous lichens Xanthoria parietina was monitored during two years at a quarterly frequency, in 3 sites of contrasted anthropic influence. The impact of the meteorological factors (temperature, relative humidity, rainfall, wind speed) was first estimated through principal component analysis, and then by stepwise multilinear regressions to include wind directions. The pollutants levels reflected the proximity of atmospheric emissions, in particular from a large industrial harbor. High humidity and mild temperatures, and in a lower extent low wind speed and rainfall, also favored higher concentration levels. The contributions of these meteorological aspects became minor when including wind direction, especially when approaching major emission sources. The bioaccumulation integration time towards meteorological variations was on a seasonal basis (1–2 months) but the wind direction and thus local emissions also relied on a longer time scale (12 months). This showed that the contribution of meteorological conditions may be prevalent in remote places, while secondary in polluted areas, and should be definitely taken into account regarding long-term lichen biomonitoring and inter-annual comparisons. In the same time, a quadruple sampling in each site revealed a high homogeneity among supporting tree species and topography. The resulting uncertainty, including sampling, preparation and analysis was below 30% when comfortable analytical conditions were achieved. Finally, the occurrence of unexpected events such as a major forest fire, permitted to evaluate that this type of short, although intense, events did not have a strong influence on PAH and metals bioaccumulation by lichen.